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Protein

GC-rich sequence DNA-binding factor 2

Gene

GCFC2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Factor that represses transcription. It binds to the GC-rich sequences (5'-GCGGGGC-3') present in the epidermal growth factor receptor, beta-actin, and calcium-dependent protease promoters. Involved in pre-mRNA splicing through regulating spliceosome C complex formation. May play a role during late-stage splicing events and turnover of excised inrons.1 Publication

GO - Molecular functioni

GO - Biological processi

  • negative regulation of transcription, DNA-templated Source: UniProtKB
  • negative regulation of transcription from RNA polymerase II promoter Source: NTNU_SB
  • regulation of transcription, DNA-templated Source: UniProtKB
  • spliceosomal complex assembly Source: UniProtKB
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

mRNA processing, mRNA splicing, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000005436-MONOMER.
ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
GC-rich sequence DNA-binding factor 2
Alternative name(s):
GC-rich sequence DNA-binding factor
Transcription factor 9
Short name:
TCF-9
Gene namesi
Name:GCFC2
Synonyms:C2orf3, GCF, TCF9
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:1317. GCFC2.

Subcellular locationi

  • Nucleusnucleoplasm 1 Publication
  • Nucleusnucleolus 1 Publication

GO - Cellular componenti

  • nucleolus Source: UniProtKB
  • nucleoplasm Source: UniProtKB-SubCell
  • nucleus Source: UniProtKB
  • U2-type post-mRNA release spliceosomal complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi6936.
OpenTargetsiENSG00000005436.
PharmGKBiPA25892.

Polymorphism and mutation databases

BioMutaiGCFC2.
DMDMi118572650.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000874411 – 781GC-rich sequence DNA-binding factor 2Add BLAST781

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei16PhosphoserineCombined sources1
Modified residuei17PhosphoserineCombined sources1
Modified residuei19PhosphoserineCombined sources1
Modified residuei40PhosphoserineCombined sources1
Modified residuei96PhosphoserineCombined sources1
Modified residuei97PhosphothreonineCombined sources1
Modified residuei129PhosphoserineBy similarity1
Modified residuei174PhosphoserineCombined sources1
Modified residuei180PhosphoserineCombined sources1
Modified residuei213PhosphothreonineCombined sources1
Modified residuei214PhosphoserineCombined sources1
Modified residuei217PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiP16383.
MaxQBiP16383.
PaxDbiP16383.
PeptideAtlasiP16383.
PRIDEiP16383.

PTM databases

iPTMnetiP16383.
PhosphoSitePlusiP16383.

Expressioni

Tissue specificityi

Widely expressed in tissues and cell lines.

Gene expression databases

BgeeiENSG00000005436.
CleanExiHS_C2orf3.
ExpressionAtlasiP16383. baseline and differential.
GenevisibleiP16383. HS.

Interactioni

Subunit structurei

Found in the Intron Large (IL) complex, a post-mRNA release spliceosomal complex containing the excised intron, U2, U5 and U6 snRNPs, and splicing factors. Interacts with TFIP11 and DHX15.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
TFIP11Q9UBB94EBI-954074,EBI-1105213

Protein-protein interaction databases

BioGridi112797. 22 interactors.
IntActiP16383. 12 interactors.
MINTiMINT-2863474.
STRINGi9606.ENSP00000318690.

Structurei

3D structure databases

ProteinModelPortaliP16383.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili267 – 312Sequence analysisAdd BLAST46

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi116 – 122Poly-Ser7

Sequence similaritiesi

Belongs to the GCF family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG2136. Eukaryota.
ENOG410YU43. LUCA.
GeneTreeiENSGT00390000000455.
HOGENOMiHOG000112699.
HOVERGENiHBG101878.
InParanoidiP16383.
KOiK09061.
OMAiQDTWEQQ.
OrthoDBiEOG091G080I.
PhylomeDBiP16383.
TreeFamiTF315109.

Family and domain databases

InterProiIPR012890. GCFC.
IPR022783. GCFC_dom.
[Graphical view]
PANTHERiPTHR12214. PTHR12214. 1 hit.
PfamiPF07842. GCFC. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P16383-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAHRPKRTFR QRAADSSDSD GAEESPAEPG APRELPVPGS AEEEPPSGGG
60 70 80 90 100
RAQVAGLPHR VRGPRGRGRV WASSRRATKA APRADEGSES RTLDVSTDEE
110 120 130 140 150
DKIHHSSESK DDQGLSSDSS SSLGEKELSS TVKIPDAAFI QAARRKRELA
160 170 180 190 200
RAQDDYISLD VQHTSSISGM KRESEDDPES EPDDHEKRIP FTLRPQTLRQ
210 220 230 240 250
RMAEESISRN EETSEESQED EKQDTWEQQQ MRKAVKIIEE RDIDLSCGNG
260 270 280 290 300
SSKVKKFDTS ISFPPVNLEI IKKQLNTRLT LLQETHRSHL REYEKYVQDV
310 320 330 340 350
KSSKSTIQNL ESSSNQALNC KFYKSMKIYV ENLIDCLNEK IINIQEIESS
360 370 380 390 400
MHALLLKQAM TFMKRRQDEL KHESTYLQQL SRKDETSTSG NFSVDEKTQW
410 420 430 440 450
ILEEIESRRT KRRQARVLSG NCNHQEGTSS DDELPSAEMI DFQKSQGDIL
460 470 480 490 500
QKQKKVFEEV QDDFCNIQNI LLKFQQWREK FPDSYYEAFI SLCIPKLLNP
510 520 530 540 550
LIRVQLIDWN PLKLESTGLK EMPWFKSVEE FMDSSVEDSK KESSSDKKVL
560 570 580 590 600
SAIINKTIIP RLTDFVEFLW DPLSTSQTTS LITHCRVILE EHSTCENEVS
610 620 630 640 650
KSRQDLLKSI VSRMKKAVED DVFIPLYPKS AVENKTSPHS KFQERQFWSG
660 670 680 690 700
LKLFRNILLW NGLLTDDTLQ ELGLGKLLNR YLIIALLNAT PGPDVVKKCN
710 720 730 740 750
QVAACLPEKW FENSAMRTSI PQLENFIQFL LQSAHKLSRS EFRDEVEEII
760 770 780
LILVKIKALN QAESFIGEHH LDHLKSLIKE D
Length:781
Mass (Da):89,385
Last modified:November 28, 2006 - v2
Checksum:i38D34EE4442EB3DF
GO
Isoform 2 (identifier: P16383-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     169-207: GMKRESEDDPESEPDDHEKRIPFTLRPQTLRQRMAEESI → V

Note: No experimental confirmation available.
Show »
Length:743
Mass (Da):84,847
Checksum:iE0187138CD59CE75
GO
Isoform 3 (identifier: P16383-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     207-213: ISRNEET → SMDLPIY
     214-779: Missing.

Show »
Length:215
Mass (Da):23,613
Checksum:iBE28FB823AF92EB5
GO
Isoform 4 (identifier: P16383-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     240-254: ERDIDLSCGNGSSKV → INITTGNSPLTPEGV
     255-781: Missing.

Show »
Length:254
Mass (Da):28,048
Checksum:iF2466348136E2B62
GO

Sequence cautioni

The sequence AAA35598 differs from that shown. Contaminating sequence. The N-terminus matches the 2q37.3 region.Curated
The sequence AAA35598 differs from that shown. Reason: Frameshift at position 147.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05100532P → A.1 PublicationCorresponds to variant rs7559767dbSNPEnsembl.1
Natural variantiVAR_051006249N → S.Corresponds to variant rs7560262dbSNPEnsembl.1
Natural variantiVAR_051007316Q → E.Corresponds to variant rs6742946dbSNPEnsembl.1
Natural variantiVAR_051008594T → A.Corresponds to variant rs6722682dbSNPEnsembl.1
Natural variantiVAR_051009724E → D.Corresponds to variant rs17690300dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_021798169 – 207GMKRE…AEESI → V in isoform 2. 1 PublicationAdd BLAST39
Alternative sequenceiVSP_054362207 – 213ISRNEET → SMDLPIY in isoform 3. 1 Publication7
Alternative sequenceiVSP_054363214 – 779Missing in isoform 3. 1 PublicationAdd BLAST566
Alternative sequenceiVSP_057398240 – 254ERDID…GSSKV → INITTGNSPLTPEGV in isoform 4. 1 PublicationAdd BLAST15
Alternative sequenceiVSP_057399255 – 781Missing in isoform 4. 1 PublicationAdd BLAST527

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M29204 mRNA. Translation: AAA35598.1. Sequence problems.
EF158467 mRNA. Translation: ABO84856.1.
EF158468 mRNA. Translation: ABO84857.1.
AC005034 Genomic DNA. Translation: AAY14973.1.
CH471053 Genomic DNA. Translation: EAW99586.1.
BC064559 mRNA. Translation: AAH64559.1.
CCDSiCCDS1961.1. [P16383-1]
CCDS62943.1. [P16383-3]
PIRiA33633.
RefSeqiNP_001188263.1. NM_001201334.1.
NP_001188264.1. NM_001201335.1. [P16383-3]
NP_003194.3. NM_003203.4. [P16383-1]
UniGeneiHs.303808.
Hs.662279.
Hs.710597.

Genome annotation databases

EnsembliENST00000321027; ENSP00000318690; ENSG00000005436. [P16383-1]
ENST00000409857; ENSP00000386552; ENSG00000005436. [P16383-2]
ENST00000470503; ENSP00000474481; ENSG00000005436. [P16383-3]
ENST00000541687; ENSP00000437767; ENSG00000005436. [P16383-4]
GeneIDi6936.
KEGGihsa:6936.
UCSCiuc002sno.4. human. [P16383-1]
uc061lbc.1. human.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M29204 mRNA. Translation: AAA35598.1. Sequence problems.
EF158467 mRNA. Translation: ABO84856.1.
EF158468 mRNA. Translation: ABO84857.1.
AC005034 Genomic DNA. Translation: AAY14973.1.
CH471053 Genomic DNA. Translation: EAW99586.1.
BC064559 mRNA. Translation: AAH64559.1.
CCDSiCCDS1961.1. [P16383-1]
CCDS62943.1. [P16383-3]
PIRiA33633.
RefSeqiNP_001188263.1. NM_001201334.1.
NP_001188264.1. NM_001201335.1. [P16383-3]
NP_003194.3. NM_003203.4. [P16383-1]
UniGeneiHs.303808.
Hs.662279.
Hs.710597.

3D structure databases

ProteinModelPortaliP16383.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112797. 22 interactors.
IntActiP16383. 12 interactors.
MINTiMINT-2863474.
STRINGi9606.ENSP00000318690.

PTM databases

iPTMnetiP16383.
PhosphoSitePlusiP16383.

Polymorphism and mutation databases

BioMutaiGCFC2.
DMDMi118572650.

Proteomic databases

EPDiP16383.
MaxQBiP16383.
PaxDbiP16383.
PeptideAtlasiP16383.
PRIDEiP16383.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000321027; ENSP00000318690; ENSG00000005436. [P16383-1]
ENST00000409857; ENSP00000386552; ENSG00000005436. [P16383-2]
ENST00000470503; ENSP00000474481; ENSG00000005436. [P16383-3]
ENST00000541687; ENSP00000437767; ENSG00000005436. [P16383-4]
GeneIDi6936.
KEGGihsa:6936.
UCSCiuc002sno.4. human. [P16383-1]
uc061lbc.1. human.

Organism-specific databases

CTDi6936.
DisGeNETi6936.
GeneCardsiGCFC2.
HGNCiHGNC:1317. GCFC2.
MIMi189901. gene.
neXtProtiNX_P16383.
OpenTargetsiENSG00000005436.
PharmGKBiPA25892.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2136. Eukaryota.
ENOG410YU43. LUCA.
GeneTreeiENSGT00390000000455.
HOGENOMiHOG000112699.
HOVERGENiHBG101878.
InParanoidiP16383.
KOiK09061.
OMAiQDTWEQQ.
OrthoDBiEOG091G080I.
PhylomeDBiP16383.
TreeFamiTF315109.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000005436-MONOMER.
ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.

Miscellaneous databases

ChiTaRSiGCFC2. human.
GeneWikiiC2orf3.
GenomeRNAii6936.
PROiP16383.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000005436.
CleanExiHS_C2orf3.
ExpressionAtlasiP16383. baseline and differential.
GenevisibleiP16383. HS.

Family and domain databases

InterProiIPR012890. GCFC.
IPR022783. GCFC_dom.
[Graphical view]
PANTHERiPTHR12214. PTHR12214. 1 hit.
PfamiPF07842. GCFC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiGCFC2_HUMAN
AccessioniPrimary (citable) accession number: P16383
Secondary accession number(s): A4UHQ8
, A4UHQ9, O95032, Q53TY0, Q6P2F2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: November 28, 2006
Last modified: November 30, 2016
This is version 161 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.