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Protein

GC-rich sequence DNA-binding factor 2

Gene

GCFC2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

Keywordsi

Molecular functionDNA-binding, Repressor
Biological processmRNA processing, mRNA splicing, Transcription, Transcription regulation

Enzyme and pathway databases

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

EuPathDBiHostDB:ENSG00000005436.13
HGNCiHGNC:1317 GCFC2
MIMi189901 gene
neXtProtiNX_P16383

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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
ProteomicsDBi53347
53348 [P16383-2]

PTM databases

iPTMnetiP16383
PhosphoSitePlusiP16383

Expressioni

Tissue specificityi

Widely expressed in tissues and cell lines.

Gene expression databases

BgeeiENSG00000005436 Expressed in 209 organ(s), highest expression level in kidney
CleanExiHS_C2orf3
ExpressionAtlasiP16383 baseline and differential
GenevisibleiP16383 HS

Organism-specific databases

HPAiHPA077882

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, 24 interactors
IntActiP16383, 12 interactors
STRINGi9606.ENSP00000318690

Structurei

3D structure databases

ProteinModelPortaliP16383
SMRiP16383
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
OMAiLQDTHRS
OrthoDBiEOG091G080I
PhylomeDBiP16383
TreeFamiTF315109

Family and domain databases

InterProiView protein in InterPro
IPR012890 GCFC
IPR022783 GCFC_dom
PANTHERiPTHR12214 PTHR12214, 1 hit
PfamiView protein in Pfam
PF07842 GCFC, 1 hit

Sequences (4+)i

Sequence statusi: Complete.

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

This entry has 4 described isoforms and 5 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 5 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
C9JII4C9JII4_HUMAN
GC-rich sequence DNA-binding factor...
GCFC2
185Annotation score:
H7C335H7C335_HUMAN
GC-rich sequence DNA-binding factor...
GCFC2
199Annotation score:
S4R465S4R465_HUMAN
GC-rich sequence DNA-binding factor...
GCFC2
43Annotation score:
S4R461S4R461_HUMAN
GC-rich sequence DNA-binding factor...
GCFC2
27Annotation score:
S4R3C1S4R3C1_HUMAN
GC-rich sequence DNA-binding factor...
GCFC2
35Annotation score:

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 → A1 PublicationCorresponds to variant dbSNP:rs7559767Ensembl.1
Natural variantiVAR_051006249N → S. Corresponds to variant dbSNP:rs7560262Ensembl.1
Natural variantiVAR_051007316Q → E. Corresponds to variant dbSNP:rs6742946Ensembl.1
Natural variantiVAR_051008594T → A. Corresponds to variant dbSNP:rs6722682Ensembl.1
Natural variantiVAR_051009724E → D. Corresponds to variant dbSNP:rs17690300Ensembl.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

Similar proteinsi

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
SMRiP16383
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112797, 24 interactors
IntActiP16383, 12 interactors
STRINGi9606.ENSP00000318690

PTM databases

iPTMnetiP16383
PhosphoSitePlusiP16383

Polymorphism and mutation databases

BioMutaiGCFC2
DMDMi118572650

Proteomic databases

EPDiP16383
MaxQBiP16383
PaxDbiP16383
PeptideAtlasiP16383
PRIDEiP16383
ProteomicsDBi53347
53348 [P16383-2]

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
EuPathDBiHostDB:ENSG00000005436.13
GeneCardsiGCFC2
HGNCiHGNC:1317 GCFC2
HPAiHPA077882
MIMi189901 gene
neXtProtiNX_P16383
OpenTargetsiENSG00000005436
PharmGKBiPA25892
GenAtlasiSearch...

Phylogenomic databases

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

Enzyme and pathway databases

ReactomeiR-HSA-72163 mRNA Splicing - Major Pathway

Miscellaneous databases

ChiTaRSiGCFC2 human
GeneWikiiC2orf3
GenomeRNAii6936
PROiPR:P16383
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000005436 Expressed in 209 organ(s), highest expression level in kidney
CleanExiHS_C2orf3
ExpressionAtlasiP16383 baseline and differential
GenevisibleiP16383 HS

Family and domain databases

InterProiView protein in InterPro
IPR012890 GCFC
IPR022783 GCFC_dom
PANTHERiPTHR12214 PTHR12214, 1 hit
PfamiView protein in Pfam
PF07842 GCFC, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiGCFC2_HUMAN
AccessioniPrimary (citable) accession number: P16383
Secondary accession number(s): A4UHQ8
, A4UHQ9, O95032, Q53TY0, Q6P2F2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: November 28, 2006
Last modified: November 7, 2018
This is version 172 of the entry and version 2 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  2. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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