GO:0000010

MF

trans-hexaprenyltranstransferase activity

Catalysis of the reaction: all-trans-hexaprenyl diphosphate + isopentenyl diphosphate = all-trans-heptaprenyl diphosphate + diphosphate.

PDSS1, PDSS2

GO:0000014

MF

single-stranded DNA endodeoxyribonuclease activity

Catalysis of the hydrolysis of ester linkages within a single-stranded deoxyribonucleic acid molecule by creating internal breaks.

ERCC1, MRE11A, RAD50, ERCC4, DCLRE1C

GO:0000016

MF

lactase activity

Catalysis of the reaction: lactose + H2O = D-glucose + D-galactose.

LCT

GO:0000026

MF

alpha-1,2-mannosyltransferase activity

Catalysis of the transfer of a mannose residue to an oligosaccharide, forming an alpha-(1->2) linkage.

ALG9

GO:0000030

MF

mannosyltransferase activity

Catalysis of the transfer of a mannosyl group to an acceptor molecule, typically another carbohydrate or a lipid.

DPY19L2, DPY19L3, DPY19L4, ALG9, POMT1

GO:0000033

MF

alpha-1,3-mannosyltransferase activity

Catalysis of the transfer of a mannose residue to an oligosaccharide, forming an alpha-(1->3) linkage.

ALG8

GO:0000036

MF

ACP phosphopantetheine attachment site binding involved in fatty acid biosynthetic process

Interacting selectively and non-covalently with the attachment site of the phosphopantetheine prosthetic group of an acyl carrier protein (ACP) as part of the process of fatty acid biosynthesis.

NDUFAB1

GO:0000049

MF

tRNA binding

Interacting selectively and non-covalently with transfer RNA.

PTCD1, TRMU, FARS2, SSB, RPL35A, RARS, YARS, EEF1A1, NSUN2, IFIT5, KARS, EARS2, TRMT1L, TRNT1, THUMPD3, SEPSECS, EIF2AK4, FARSA

GO:0000062

MF

fatty-acyl-CoA binding

Interacting selectively and non-covalently with acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group.

ACOT7, ACOX3, ECI2, SCP2, SOAT1, HMGCL, ACADSB, ACADVL, ALDH6A1, ACOX1, ACBD5, ACOX2, ACBD3

GO:0000064

MF

L-ornithine transmembrane transporter activity

Enables the transfer of L-ornithine from one side of a membrane to the other. L-ornithine is 2,5-diaminopentanoic acid.

SLC25A15

GO:0000095

MF

S-adenosyl-L-methionine transmembrane transporter activity

Enables the transfer of S-adenosylmethionine from one side of a membrane to the other. S-adenosylmethionine is S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism.

SLC25A26

GO:0000104

MF

succinate dehydrogenase activity

Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor.

SDHB, SDHA, SDHC

GO:0000146

MF

microfilament motor activity

Catalysis of movement along a microfilament, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP).

MYO1C, MYO1D, MYH9, MYO1E, MYO9B, MYH2, MYO5B, MYO5A, MYH4

GO:0000149

MF

SNARE binding

Interacting selectively and non-covalently with a SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein.

GOSR2, STX7, EXOC3, VAMP4, SEC22B, STX11, SNAPIN, SYT1, STX2, VAMP7, GABARAPL2, STXBP1, VAMP2, TNFAIP2, STX4, STX3, VAMP3, SEC22A, ANKRD27, TRIM9, CAPN10, VTI1B

GO:0000150

MF

recombinase activity

Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA.

RAD51C, RAD51D, RAD51

GO:0000155

MF

phosphorelay sensor kinase activity

Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.

KCNH2

GO:0000166

MF

nucleotide binding

Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

RBM47, IGF2BP3, HNRNPDL, U2SURP, SYNJ2, POLR2D, RBFOX2, HNRNPR, SYNJ1, ORC5, SYNCRIP, REV3L, SRSF10, CRCP, DHRS3, DXO, TMEM63A, SCAF4, CELF2, PARN, CNOT4, PTBP3, TYMS, SSB, HSP90AA1, HNRNPC, SNRPA, HNRNPA1, POLA1, PYGM, HNRNPL, NT5E, HNRNPA2B1, SFPQ, EIF4B, PTBP1, POLD1, RBMS1, TIA1, HNRNPH3, HNRNPH1, FUS, RBMX, MATR3, VDAC2, RBM25, HINT1, FHIT, HDGF, HNRNPA3, HNRNPM, RBM5, RCAN1, HNRNPH2, EIF3B, RPL23A, TRA2B, RBM6, GPSM2, RBM3, SRSF2, EWSR1, SRSF11, POLE, SRSF1, GRSF1, TARDBP, SRSF9, SRSF5, SRSF6, TRA2A, CIRBP, HNRNPD, RBM39, ELAVL3, ZNF638, SART3, NONO, RNPS1, RBMS2, ELAVL1, CRY1, MRPL23, SNRNP35, CPEB4, LARP7, PABPC1L, NCBP3, RBM48, RBM26, SLC27A4, SLC27A1, RBPMS2, RBM43, LARP4, NOL8, CPEB2, PABPN1, ALYREF, CHD1L, PPARGC1B, RBM45, TNRC6A, CPEB3, NUP35, ZCRB1, ENOX1, PPIL4, SREK1, PSPC1, TAF15, RBPMS, MSI2, DAZAP1, RBM33, RBM17, RNPC3, RBM15, SPEN, HNRNPAB, CDC6, RBM4B, LARP6, RBM4, RBM24, HINT2, POLDIP3, NIFK, SLIRP, RBM38, UPF3A, PABPC3, ESRP2, TNRC6C, RAVER2, NOX4, HINT3, PRTFDC1, RBM22, RBFOX1, SLTM, TRNAU1AP, AKAP7, MYEF2, PPARGC1A, NXF1, PUF60, PTBP2, G3BP2, PPIE, SCAF8, TNRC6B, VDAC3, SLC27A6, LEMD3, RBMX2, RRP7A, SF3B6, R3HCC1, KIAA0430, RBM8A, IGF2BP2

GO:0000171

MF

ribonuclease MRP activity

Catalysis of the site-specific cleavage of RNA by a catalytic RNA-mediated mechanism; substrates include the A3 site in the ITS1 of pre-rRNA.

POP4

GO:0000175

MF

3'-5'-exoribonuclease activity

Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.

EXOSC9, EXOSC2, EXOSC7, PNPT1, ISG20, EXOSC4, EXOSC3, CNOT7, DIS3, REXO2

GO:0000179

MF

rRNA (adenine-N6,N6-)-dimethyltransferase activity

Catalysis of the dimethylation two adjacent A residues in the loop closing the 3'-terminal stem of the 18S rRNA, using S-adenosyl-L-methionine as a methyl donor.

DIMT1

GO:0000182

MF

rDNA binding

Interacting selectively and non-covalently with DNA sequences encoding ribosomal RNA.

H2AFY, TSPYL2

GO:0000213

MF

tRNA-intron endonuclease activity

Catalysis of the endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron.

TSEN15

GO:0000215

MF

tRNA 2'-phosphotransferase activity

Catalysis of the reaction: 2'-phospho-[ligated tRNA] + NAD+ = mature tRNA + ADP ribose 1'',2''-phosphate + nicotinamide + H2O. This reaction is the transfer of the splice junction 2-phosphate from ligated tRNA to NAD+ to produce ADP-ribose 1'-2' cyclic phosphate.

TRPT1

GO:0000246

MF

delta24(24-1) sterol reductase activity

Catalysis of the reaction: ergosterol + NADP(+) = ergosta-5,7,22,24(24(1))-tetraen-3beta-ol + H(+) + NADPH.

DHCR24

GO:0000247

MF

C-8 sterol isomerase activity

Catalysis of the reaction which results in unsaturation at C-7 in the B ring of sterols.

EBP

GO:0000248

MF

C-5 sterol desaturase activity

Catalysis of the reaction: 5,7,24(28)-ergostatrienol + O2 + NADPH = 5,7,22,24(28)-ergostatetraenol + 2 H2O + NADP+.

FADS1, SC5D

GO:0000250

MF

lanosterol synthase activity

Catalysis of the reaction: (S)-2,3-epoxysqualene = lanosterol. This is a cyclization reaction that forms the sterol nucleus.

LSS

GO:0000252

MF

C-3 sterol dehydrogenase (C-4 sterol decarboxylase) activity

Catalysis of the reaction: 3-beta-hydroxy-4-beta-methyl-5-alpha-cholesta-8,24-dien-4-alpha-carboxylate + NAD(P)+ = 4-alpha-methyl-5-alpha-cholesta-8,24-dien-3-one + CO2 + NAD(P)H.

NSDHL

GO:0000253

MF

3-keto sterol reductase activity

Catalysis of the reaction: a 3-beta-hydroxyl sterol + NADP+ = a 3-keto sterol + NADPH + H(+).

HSD17B7, DHRS4

GO:0000254

MF

C-4 methylsterol oxidase activity

Catalysis of the reaction: 4,4-dimethyl-5-alpha-cholesta-8,24-dien-3-beta-ol + NAD(P)H + H(+) + O2 = 4-beta-hydroxymethyl-4-alpha-methyl-5-alpha-cholesta-8,24-dien-3-beta-ol + NAD(P)+ + H2O.

CH25H, MSMO1

GO:0000285

MF

1-phosphatidylinositol-3-phosphate 5-kinase activity

Catalysis of the reaction: a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + ADP + 2 H(+).

PIP5K1B, PIKFYVE

GO:0000287

MF

magnesium ion binding

Interacting selectively and non-covalently with magnesium (Mg) ions.

CIB4, ILVBL, GTPBP10, EYA2, PDXK, MAP2K7, MAST4, MAP3K7, ATP8B1, IDH3B, OPA1, ATP9A, ERN1, RPS6KA5, PPM1B, IDH1, DXO, FARS2, TDP2, LATS1, NUDT3, ENO1, ENO2, NUDT7, TOP2A, PRPS2, ENO3, MTHFD2, PKM, NME1, COMT, S100P, IMPA1, WEE1, ADSS, DUT, PCK1, HMGCL, PGM1, SNCA, FEN1, MAP3K8, ABL2, MSH2, GCLC, IDH2, INPP1, PAPOLA, MSH6, ADPRH, GEM, SIK1, PTEN, PRPS1, NCS1, GNAI1, SRPK2, ARF1, STK4, ITPK1, STK38, RPS6KA2, RPS6KA1, STK11, CDC42BPA, MAST2, ENOSF1, CLYBL, ADSSL1, XXYLT1, ATP8B4, DYRK2, NUDT16, PGM2, SRPK1, MAP3K5, TREX2, PINK1, SIK2, PPA2, WNK1, MTG2, PIF1, DCTPP1, RRAGC, NEK6, PRTFDC1, AASDHPPT, MTPAP, SPHK1, ZAK, MARK1, NLK, NUDT5, ATP11B, STK38L, SIK3, FAN1, CDC42BPB, IRAK3

GO:0000293

MF

ferric-chelate reductase activity

Catalysis of the reaction: 2 Fe2+ + NAD+ = 2 Fe3+ + NADH + H(+).

CYBRD1

GO:0000295

MF

adenine nucleotide transmembrane transporter activity

Catalysis of the transfer of adenine nucleotides (AMP, ADP, and ATP) from one side of the membrane to the other.

SLC25A17

GO:0000298

MF

endopolyphosphatase activity

Catalysis of the reaction: polyphosphate + n H2O = (n+1) oligophosphate. The product contains 4 or 5 phosphate residues.

NUDT3, NUDT10, NUDT11

GO:0000309

MF

nicotinamide-nucleotide adenylyltransferase activity

Catalysis of the reaction: ATP + nicotinamide nucleotide = diphosphate + NAD+.

NMNAT3

GO:0000339

MF

RNA cap binding

Interacting selectively and non-covalently with a 7-methylguanosine (m7G) group or derivative located at the 5' end of an RNA molecule.

EIF4G3, EIF4E2, EIF4E, EIF4A1, NCBP1, LARP1

GO:0000340

MF

RNA 7-methylguanosine cap binding

Interacting selectively and non-covalently with the 7-methylguanosine group added cotranscriptionally to the 5' end of RNA molecules transcribed by polymerase II.

NCBP3, AGO2

GO:0000384

MF

first spliceosomal transesterification activity

Catalysis of the first transesterification reaction of spliceosomal mRNA splicing. The intron branch site adenosine is the nucleophile attacking the 5' splice site, resulting in cleavage at this position. In cis splicing, this is the step that forms a lariat structure of the intron RNA, while it is still joined to the 3' exon.

RBMX2

GO:0000386

MF

second spliceosomal transesterification activity

Catalysis of the second transesterification reaction of spliceosomal mRNA splicing. Ligation of the two exons occurs via a transesterification reaction where the free 3'-hydroxyl group of the 5' exon is the nucleophile attacking the 3' splice site. Non-expressed sequences are now detached from the exons. In cis splicing, the intron is in a lariat structure.

PRPF18

GO:0000400

MF

four-way junction DNA binding

Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices.

HMGB3, RAD51C, RAD51D, HMGB1, YY1, HMGB2, MSH2, MSH6, RAD51

GO:0000403

MF

Y-form DNA binding

Interacting selectively and non-covalently with segment of DNA shaped like a Y. This shape occurs when DNA contains a region of paired double-stranded DNA on one end and a region of unpaired DNA strands on the opposite end.

MSH2, RAD18

GO:0000404

MF

heteroduplex DNA loop binding

Interacting selectively and non-covalently with DNA containing a loop. A loop occurs when DNA contains a large insertion or deletion that causes a region of unpaired single-stranded DNA to loop out, while the rest of the DNA is in a paired double-stranded configuration.

MSH2, XPC

GO:0000405

MF

bubble DNA binding

Interacting selectively and non-covalently with DNA that contains a bubble. A bubble occurs when DNA contains a region of unpaired, single-stranded DNA flanked on both sides by regions of paired, double-stranded DNA.

RECQL4, HMGB1, BLM, XPC, NEIL3

GO:0000406

MF

double-strand/single-strand DNA junction binding

Interacting selectively and non-covalently with a region of DNA that contains double-stranded DNA flanked by a region of single-stranded DNA.

MSH2

GO:0000701

MF

purine-specific mismatch base pair DNA N-glycosylase activity

Catalysis of the removal of purines present in mismatches, especially opposite oxidized purines, by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic (AP) site.

PCNA

GO:0000703

MF

oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity

Catalysis of the removal oxidized pyrimidine bases by cleaving the N-C1' glycosidic bond between the oxidized pyrimidine and the deoxyribose sugar. The reaction involves formation of a covalent enzyme-pyrimidine base intermediate. Release of the enzyme and free base by a beta-elimination or a beta, gamma-elimination mechanism results in the cleavage of the DNA backbone 3' of the apyrimidinic (AP) site.

NTHL1, SMUG1

GO:0000773

MF

phosphatidyl-N-methylethanolamine N-methyltransferase activity

Catalysis of the reaction: S-adenosyl-L-methionine + phosphatidyl-N-methylethanolamine = S-adenosyl-L-homocysteine + phosphatidyl-N-dimethylethanolamine.

PEMT

GO:0000774

MF

adenyl-nucleotide exchange factor activity

Stimulates the hydrolysis and exchange of adenyl nucleotides by other proteins.

BAG2, PFN1, HSPH1, GRPEL1, BAG5

GO:0000822

MF

inositol hexakisphosphate binding

Interacting selectively and non-covalently with inositol hexakisphosphate.

ITPR3

GO:0000827

MF

inositol-1,3,4,5,6-pentakisphosphate kinase activity

Catalysis of the reaction: ATP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate = ADP + diphospho-1D-myo-inositol tetrakisphosphate. The isomeric configuration of diphospho-1D-myo-inositol tetrakisphosphate is unknown.

PPIP5K1, IP6K2

GO:0000828

MF

inositol hexakisphosphate kinase activity

Catalysis of the reaction: ATP + 1D-myo-inositol 1,2,3,4,5,6-hexakisphosphate = ADP + diphospho-1D-myo-inositol-pentakisphosphate. The isomeric configuration of diphospho-1D-myo-inositol-pentakisphosphate (PP-IP5) is unknown.

PPIP5K1, IP6K2

GO:0000829

MF

inositol heptakisphosphate kinase activity

Catalysis of the reaction: ATP + diphospho-1D-myo-inositol-pentakisphosphate = ADP + bis(diphospho)-1D-myo-inositol-tetrakisphosphate. The isomeric configurations of the diphospho-1D-myo-inositol-pentakisphosphate (PP-IP5) and bis(diphospho)-1D-myo-inositol-tetrakisphosphate (bis-PP-IP4) are unknown.

PPIP5K1, IP6K2

GO:0000832

MF

inositol hexakisphosphate 5-kinase activity

Catalysis of the reaction: ATP + 1D-myo-inositol 1,2,3,4,5,6-hexakisphosphate = ADP + 5-diphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate.

PPIP5K1, IP6K2

GO:0000900

MF

translation repressor activity, nucleic acid binding

Antagonizes the ribosome-mediated translation of mRNA into a polypeptide via direct binding (through a selective and non-covalent interaction) to nucleic acid.

PURA, CPEB4, CPEB2, CPEB3

GO:0000975

MF

regulatory region DNA binding

Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair.

IRF6, NFKB1, HMGA2, RUNX1

GO:0000976

MF

transcription regulatory region sequence-specific DNA binding

Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.

ARNTL, NR5A2, SOX12, PARK2, THRA, EGR1, ATF3, ATF6, NFKB1, SFPQ, DDIT3, POU5F1, SOX4, HDAC1, NFE2L1, NONO, JMJD1C, ZNF658, PSPC1, PITX2, SUV39H2, NFE2L3

GO:0000977

MF

RNA polymerase II regulatory region sequence-specific DNA binding

Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.

ACTN4, H2AFY, ZBED1, ZFY, GLI3, NME1, ZFX, TAL1, CEBPB, EGR1, ATF1, ATF3, ATF4, ATF6, NFKB1, NR1D1, HNF1A, LMO2, RXRB, RORA, ETV5, BCL6, GATA4, NKX2-1, PRDM15, FOXK1, ZBED6, RUNX1, RELB, SATB1, MEF2A, SP3, RELA, MEF2C, DLX2, FOXC1, ZNF211, RUNX3, CUX1, MEF2D, POU6F1, ARID5B, ZMYND11, HLF, NFIL3, NFXL1, ZSCAN2, GATAD2A, AEBP1, ZNF548, KAT2B, GATA6, ZBED6CL, ZNF419, HES6, PURB, PHF12, MNT, ARID3A, IKZF5, ZNF552, ZNF586, H2AFY2, ZBTB4, MLX, TRPS1, ELF5, PLAGL1

GO:0000978

MF

RNA polymerase II core promoter proximal region sequence-specific DNA binding

Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.

E2F8, MEIS1, NR5A2, NFIB, FOXP2, PER1, KDM6A, ZNF264, HOXA2, SMAD6, MITF, ZNF253, ZNF217, NFAT5, ZBTB7A, MBD3, ACTL6A, FOS, MYC, ESR1, NR3C1, JUN, PGR, HNRNPC, NFIC, H2AFZ, GLI2, GLI3, MYBL1, MYBL2, AR, IRF1, EGR2, ESRRA, SKI, SKIL, ETS2, FOSL1, FOSL2, TCF4, TCF3, MUC1, CREB1, GCFC2, JUNB, JUND, CEBPB, ATF3, ATF4, ELK1, NR1D1, MZF1, HOXA10, OTX2, DDIT3, SREBF1, PBX1, STAT3, ELK3, RFX2, RFX5, CEBPD, MEOX1, ETV1, ASCL1, SMARCA4, ZNF138, FOSB, NR1H2, DLX5, FOXL2, ACTB, YBX1, ELF3, SMAD3, TFAM, HSF1, INSM1, MEF2A, HHEX, CEBPZ, ZNF85, ZNF117, ZNF92, RELA, MXD1, MEF2C, GABPA, PAX8, PPARA, RBBP4, SREBF2, NFATC2, SMAD4, HDAC1, RUNX2, NFYC, ZNF273, MEF2D, CHD4, MTF1, NFATC4, NCOA2, SMAD2, SMAD1, ZIC1, ZNF141, IFI16, ZNF506, PLAG1, ZNF562, AKNA, CTCFL, SMARCC2, ZNF502, ZNF675, JDP2, NR4A3, HDAC2, SMARCC1, ZNF486, TCF12, PITX2, BCL11A, ZNF430, ZNF395, EBF2, PATZ1, TCF7L2, ZNF331, EHF, GRHL1, ZNF492, CHD7, ZNF639, ZNF148, KLF13, NFE2L3, PAXBP1, MAFB

GO:0000979

MF

RNA polymerase II core promoter sequence-specific DNA binding

Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery.

H2AFY, FOS, H2AFZ, TAL1, CEBPB, NR4A2, YAP1, STAT5B, MAZ, SOX8, H3F3A, HSF1, SP3, PAX8, EP300, RUNX2, MTF1, SUZ12, SMAD1, EZH2, NFIL3, NLRC5, GATA6, WBP2, SMAD5, ZNF335, SMYD3, HEYL, ZNF277, RUVBL2

GO:0000980

MF

RNA polymerase II distal enhancer sequence-specific DNA binding

Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.

NR5A2, BACH1, PAX4, NFATC1, MBD3, ACTL6A, JUN, HNRNPC, HOXB5, H2AFZ, HIVEP1, CREB1, TAL1, NFKB1, SFPQ, SMARCA4, ACTB, H3F3A, RELA, REL, ZBTB16, MEF2C, RBBP4, HDAC1, NFE2L1, CHD4, NONO, SMARCC2, HDAC2, SMARCC1, MED12, NR1H4, BACH2, RUVBL2

GO:0000981

MF

RNA polymerase II transcription factor activity, sequence-specific DNA binding

Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.

NFIB, BHLHE40, FOXP2, SOX15, ZMYM6, TP53, JUN, ETS1, JUNB, JUND, TAL1, XBP1, ATF4, LMO2, PHB, BMPR1A, ERF, FOXG1, SOX8, FOXL2, GTF2I, ELF3, SIM1, FOXK1, FOXO4, RELB, POU5F1, MEF2A, SP3, MEF2C, FOXM1, FOXO1, FOXC1, RUNX3, RUNX2, TFDP1, SIM2, ZMYM3, MEF2D, PCBP1, TWIST1, QRICH1, ZBED5, ZNF518A, EPM2AIP1, FOXP4, ZBED8, KIAA1958, BHLHE22, ZSCAN18, GATA6, ZNF274, ZNF641, CDC5L, EPAS1, FOXP3, ZNF518B, PEG3, FOXP1, ZMYM2, ZMYM5, ELF5, FOXJ3, HIF3A

GO:0000982

MF

transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding

Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.

ARNTL, FOS, JUN, ETS1, FOSL1, FOSL2, ATF3, FOSB, ARNTL2, JDP2

GO:0000983

MF

transcription factor activity, RNA polymerase II core promoter sequence-specific

Interacting selectively and non-covalently with a specific DNA sequence in an RNA polymerase II (Pol II) core promoter, the region composed of the transcription start site and binding sites for transcription factors of the Pol II basal transcription machinery, in order to modulate transcription by Pol II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.

SMAD3, RELA, MEF2C, HEYL, HEY1

GO:0000987

MF

core promoter proximal region sequence-specific DNA binding

Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon.

KLF4, SMAD3, SP3, SMAD4, CREBBP, UHRF1

GO:0000988

MF

transcription factor activity, protein binding

Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.

SMAD3, SMAD4, HEYL, HEY1

GO:0000989

MF

transcription factor activity, transcription factor binding

Interacting selectively and non-covalently with a specific transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.

PER1, ASCL1, HMGA2, FOXO1, CRY1, HIF1A

GO:0000991

MF

transcription factor activity, core RNA polymerase II binding

Interacting selectively and non-covalently with an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.

GTF2F2

GO:0000993

MF

RNA polymerase II core binding

Interacting selectively and non-covalently with RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits.

BRD4, IKBKAP, ELOF1, ZNF326, CCAR2, ELP4, WAC, SMYD3, ELP3, AGO2

GO:0001010

MF

transcription factor activity, sequence-specific DNA binding transcription factor recruiting

The function of binding to a specific DNA sequence and recruiting another transcription factor to the DNA in order to modulate transcription. The recruited factor may bind DNA directly, or may be colocalized via protein-protein interactions.

KLF4

GO:0001011

MF

transcription factor activity, sequence-specific DNA binding, RNA polymerase recruiting

Interacting selectively and non-covalently with a specific DNA sequence and recruiting RNA polymerase to the DNA in order to form the preinitiation complex (PIC).

TCF4

GO:0001012

MF

RNA polymerase II regulatory region DNA binding

Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by RNA polymerase II. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.

NKX2-1, NCOA1

GO:0001025

MF

RNA polymerase III transcription factor binding

Interacting selectively and non-covalently with an RNA polymerase III transcription factor, any protein required to initiate or regulate transcription by RNA polymerase III.

HDAC4, HDAC5

GO:0001042

MF

RNA polymerase I core binding

Interacting selectively and non-covalently with RNA polymerase I core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of seventeen subunits.

ERBB2, SPTY2D1

GO:0001046

MF

core promoter sequence-specific DNA binding

Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region composed of the transcription start site and binding sites for the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon.

CHD2, H2AFY, ESR1, TP53, TOP1, ATF4, NR1D1, RORA, PPARG, SOX9, NRIP1, MEOX1, CREM, MEF2C, SOX4, KLF10, MTA1, NR1D2, ZFHX3, CRY1, NR4A3, ESR2, PROX1, THRAP3

GO:0001047

MF

core promoter binding

Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.

E2F8, ARNTL, KLF4, FOXO3, RB1, XBP1, ELK1, SFPQ, GADD45A, RBMX, NKX2-1, NOTCH1, HMGA2, HDAC4, GTF2B, HNRNPU, IRF9, E2F1, INSM1, RUNX1, RELB, EP300, MTA1, HDAC1, E2F2, MTF1, NONO, EZH2, CRY1, IFI16, CCAR1, PSPC1, HDAC2, NPAS2, MYBBP1A, FOXP3, DHX36, HDAC6, AGO2, HDAC5

GO:0001054

MF

RNA polymerase I activity

Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase I specific promoter to direct initiation and catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.

POLR1C, POLR1A, POLR2E, POLR2K, POLR2L, POLR1E, ZNRD1, POLR1D

GO:0001055

MF

RNA polymerase II activity

Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase II specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.

POLR2E, POLR2A, POLR2B, POLR2J, POLR2K, POLR2L, POLR2J2

GO:0001056

MF

RNA polymerase III activity

Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase III specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.

POLR1C, POLR3G, CRCP, POLR2E, POLR2K, POLR2L, POLR3GL, POLR3C, POLR3F, POLR3B, POLR1D, POLR3K

GO:0001069

MF

regulatory region RNA binding

Interacting selectively and non-covalently with a RNA region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair.

MBNL1

GO:0001071

MF

nucleic acid binding transcription factor activity

Interacting selectively and non-covalently with a DNA or RNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.

SOX4

GO:0001075

MF

transcription factor activity, RNA polymerase II core promoter sequence-specific binding involved in preinitiation complex assembly

Interacting selectively and non-covalently with a specific DNA sequence in an RNA polymerase II (Pol II) core promoter, the region composed of the transcription start site and binding sites for transcription factors of the Pol II basal transcription machinery, in order to promote assembly of the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase II promoter.

TAF9B, DACH1

GO:0001076

MF

transcription factor activity, RNA polymerase II transcription factor binding

Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.

ATF4, GATA4, YAP1, LHX2, SMAD4, HIF1A

GO:0001077

MF

transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding

Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.

MEIS1, NR5A2, NFIB, PLSCR1, SOX12, KLF4, TCF21, MITF, NFAT5, FOS, MYC, ESR1, NR3C1, JUN, PGR, NFIC, GLI2, GLI3, MYBL1, MYBL2, AR, IRF1, EGR2, ESRRA, FOSL1, TCF4, CREB1, JUNB, CEBPB, EGR1, ATF4, ELK1, WT1, HNF1A, NR4A1, MZF1, HOXA10, OTX2, DDIT3, SREBF1, PBX1, STAT3, ELK3, NR4A2, SOX9, CEBPD, MEOX1, ETV1, STAT5B, HMGA2, FOSB, CEBPG, NR1H2, DLX5, FOXL2, YBX1, ELF3, TFAM, MEF2A, CEBPZ, RELA, MEF2C, GABPA, PAX8, SOX4, PPARA, NFATC2, SMAD4, RUNX2, NFYC, MEF2D, MTF1, SMAD2, SMAD1, ZIC1, HLF, HIF1A, PLAG1, AKNA, CTCFL, NR4A3, CREB3L1, NR1H4, TCF12, MEIS3, PITX2, EPAS1, NUCKS1, EBF2, PATZ1, HEYL, EHF, GRHL1, ZNF639, KLF15, KLF13, MAFB, CAMTA1

GO:0001078

MF

transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding

Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.

E2F8, BHLHE40, BACH1, FOXP2, HOXA2, SNAI2, TCF21, ZNF217, ZBTB7A, ESRRA, SKI, SKIL, ETS2, TCF3, GCFC2, ATF3, NR1D1, YY1, MZF1, ASCL1, HMGA2, BTG2, HSF1, INSM1, SP3, HHEX, RELA, MXD1, PPARA, SREBF2, FOXO1, NFATC2, HES1, NFATC4, NFIL3, IFI16, NFXL1, TSHZ1, ZFPM2, JDP2, PROX1, CREBBP, BCL11A, ZBTB20, TSHZ2, DACH1, ZNF148, NFE2L3

GO:0001085

MF

RNA polymerase II transcription factor binding

Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.

WWP2, KLF4, KDM1A, NFATC1, TP53, AR, HCLS1, TAL1, XBP1, ATF4, ELK1, CTNNB1, GATA4, ID4, GSK3B, MEF2A, SMAD4, HDAC1, ANKRD1, MTDH, ZFPM2, CREBBP, GATA6, SPEN, TEAD3, DACT1, TRPS1

GO:0001087

MF

transcription factor activity, TFIIB-class binding

Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIB class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.

TCF4

GO:0001093

MF

TFIIB-class transcription factor binding

Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIB class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor.

TCF4

GO:0001094

MF

TFIID-class transcription factor binding

Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor.

ERCC1, ERCC4

GO:0001099

MF

basal RNA polymerase II transcription machinery binding

Interacting selectively and non-covalently with the basal transcription machinery for RNA polymerase II which is composed of the RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits, and the basal RNA polymerase II transcription factors, the minimal set of factors required for formation of the preinitiation complex (PIC) by the RNA polymerase.

LLPH

GO:0001102

MF

RNA polymerase II activating transcription factor binding

Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.

BHLHE40, NCOR1, JUN, RB1, EGR2, CREB1, LMO2, CTNNB1, IFI27, SMAD3, EXOSC9, EP300, CREBBP, PITX2, DUSP26, HIPK2, BEX1

GO:0001103

MF

RNA polymerase II repressing transcription factor binding

Interacting selectively and non-covalently with an RNA polymerase II transcription repressing factor, a protein involved in negative regulation of transcription.

STAT3, GTF2A2, PPARA, MTA1, HDAC1, CHD4, BBS7, BBS1, BBS10, TTC8, HDAC2, GATA6, BBS2, MKKS, TCF7L2

GO:0001104

MF

RNA polymerase II transcription cofactor activity

Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to modulate transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between regulatory transcription factors and the basal RNAP II transcription machinery.

MED19, MED7, MED14, MED21, TDG, PPARGC1B, MED12, MED30, MED15, MED20, MED4, MED17, MED9, PPARGC1A, THRAP3

GO:0001105

MF

RNA polymerase II transcription coactivator activity

Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery.

SOX12, SMARCA2, SMARCA4, MEF2A, POU3F1, SOX4, HYAL2, TRIM28, ANKRD1, NCOA1, JADE1, ZFPM2, CREBBP, MED12, WBP2, CITED4, PITX2, CITED1, CITED2, HIPK2, RERE, MKL2

GO:0001106

MF

RNA polymerase II transcription corepressor activity

Interacting selectively and non-covalently with an RNA polymerase II repressing transcription factor and also with the RNA polymerase II basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.

SIN3B, URI1, HDGF, TLE1, HDAC1, N4BP2L2, PHF12, CITED2, HEYL, RERE, UXT, ZNF451

GO:0001128

MF

RNA polymerase II transcription coactivator activity involved in preinitiation complex assembly

Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or stability of the aggregation, arrangement and bonding together of proteins on RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC). Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery.

MED6

GO:0001133

MF

RNA polymerase II transcription factor activity, sequence-specific transcription regulatory region DNA binding

Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA by RNA polymerase II and recruiting another transcription factor to the DNA in order to modulate transcription by RNAP II.

NR1H2

GO:0001135

MF

transcription factor activity, RNA polymerase II transcription factor recruiting

The function of binding to an RNA polymerase II (RNAP II) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP II.

MYBL1, MYBL2, LIF, CDC5L

GO:0001147

MF

transcription termination site sequence-specific DNA binding

Interacting selectively and non-covalently with a sequence of DNA that promotes termination by RNA polymerase. The transcribed region might be described as a gene, cistron, or operon.

SETX

GO:0001158

MF

enhancer sequence-specific DNA binding

Interacting selectively and non-covalently with a specific sequence of DNA that is part of an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter.

XBP1, YY1, HMGB2, GATA4, SOX9, LMO4, ZNF395