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P16383

- GCFC2_HUMAN

UniProt

P16383 - GCFC2_HUMAN

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Protein

GC-rich sequence DNA-binding factor 2

Gene

GCFC2

Organism
Homo sapiens (Human)
Status
Reviewed - 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

  1. RNA polymerase II core promoter proximal region sequence-specific DNA binding Source: NTNU_SB
  2. RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription Source: NTNU_SB

GO - Biological processi

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

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

mRNA processing, mRNA splicing, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

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
ProteomesiUP000005640: Chromosome 2

Organism-specific databases

HGNCiHGNC:1317. GCFC2.

Subcellular locationi

Nucleusnucleoplasm 1 Publication. Nucleusnucleolus 1 Publication

GO - Cellular componenti

  1. nucleolus Source: UniProtKB
  2. nucleus Source: UniProtKB
  3. U2-type post-mRNA release spliceosomal complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA25892.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 781781GC-rich sequence DNA-binding factor 2PRO_0000087441Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei16 – 161Phosphoserine3 Publications
Modified residuei17 – 171Phosphoserine3 Publications
Modified residuei19 – 191Phosphoserine3 Publications
Modified residuei96 – 961Phosphoserine2 Publications
Modified residuei97 – 971Phosphothreonine2 Publications
Modified residuei129 – 1291PhosphoserineBy similarity
Modified residuei213 – 2131Phosphothreonine2 Publications
Modified residuei214 – 2141Phosphoserine2 Publications
Modified residuei217 – 2171Phosphoserine2 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP16383.
PaxDbiP16383.
PRIDEiP16383.

PTM databases

PhosphoSiteiP16383.

Expressioni

Tissue specificityi

Widely expressed in tissues and cell lines.

Gene expression databases

BgeeiP16383.
CleanExiHS_C2orf3.
ExpressionAtlasiP16383. baseline and differential.
GenevestigatoriP16383.

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

Protein-protein interaction databases

BioGridi112797. 15 interactions.
IntActiP16383. 8 interactions.
MINTiMINT-2863474.
STRINGi9606.ENSP00000318690.

Structurei

3D structure databases

ProteinModelPortaliP16383.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili267 – 31246Sequence AnalysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi116 – 1227Poly-Ser

Sequence similaritiesi

Belongs to the GCF family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiNOG294271.
GeneTreeiENSGT00390000000455.
HOGENOMiHOG000112699.
HOVERGENiHBG101878.
InParanoidiP16383.
KOiK09061.
OMAiQDTWEQQ.
OrthoDBiEOG79KPGP.
PhylomeDBiP16383.
TreeFamiTF315109.

Family and domain databases

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

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. Align

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

Sequence cautioni

The sequence AAA35598.1 differs from that shown. Reason: Contaminating sequence. The N-terminus matches the 2q37.3 region.Curated
The sequence AAA35598.1 differs from that shown. Reason: Frameshift at position 147. Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti32 – 321P → A.1 Publication
Corresponds to variant rs7559767 [ dbSNP | Ensembl ].
VAR_051005
Natural varianti249 – 2491N → S.
Corresponds to variant rs7560262 [ dbSNP | Ensembl ].
VAR_051006
Natural varianti316 – 3161Q → E.
Corresponds to variant rs6742946 [ dbSNP | Ensembl ].
VAR_051007
Natural varianti594 – 5941T → A.
Corresponds to variant rs6722682 [ dbSNP | Ensembl ].
VAR_051008
Natural varianti724 – 7241E → D.
Corresponds to variant rs17690300 [ dbSNP | Ensembl ].
VAR_051009

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei169 – 20739GMKRE…AEESI → V in isoform 2. 1 PublicationVSP_021798Add
BLAST
Alternative sequencei207 – 2137ISRNEET → SMDLPIY in isoform 3. 1 PublicationVSP_054362
Alternative sequencei214 – 779566Missing in isoform 3. 1 PublicationVSP_054363Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M29204 mRNA. Translation: AAA35598.1. Sequence problems.
EF158467 mRNA. Translation: ABO84856.1.
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]
GeneIDi6936.
KEGGihsa:6936.
UCSCiuc002snn.3. human. [P16383-1]
uc002snp.4. human.

Polymorphism databases

DMDMi118572650.

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 .
AC005034 Genomic DNA. Translation: AAY14973.1 .
CH471053 Genomic DNA. Translation: EAW99586.1 .
BC064559 mRNA. Translation: AAH64559.1 .
CCDSi CCDS1961.1. [P16383-1 ]
CCDS62943.1. [P16383-3 ]
PIRi A33633.
RefSeqi NP_001188263.1. NM_001201334.1.
NP_001188264.1. NM_001201335.1. [P16383-3 ]
NP_003194.3. NM_003203.4. [P16383-1 ]
UniGenei Hs.303808.
Hs.662279.
Hs.710597.

3D structure databases

ProteinModelPortali P16383.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 112797. 15 interactions.
IntActi P16383. 8 interactions.
MINTi MINT-2863474.
STRINGi 9606.ENSP00000318690.

PTM databases

PhosphoSitei P16383.

Polymorphism databases

DMDMi 118572650.

Proteomic databases

MaxQBi P16383.
PaxDbi P16383.
PRIDEi P16383.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000321027 ; ENSP00000318690 ; ENSG00000005436 . [P16383-1 ]
ENST00000409857 ; ENSP00000386552 ; ENSG00000005436 . [P16383-2 ]
ENST00000470503 ; ENSP00000474481 ; ENSG00000005436 . [P16383-3 ]
GeneIDi 6936.
KEGGi hsa:6936.
UCSCi uc002snn.3. human. [P16383-1 ]
uc002snp.4. human.

Organism-specific databases

CTDi 6936.
GeneCardsi GC02M075880.
HGNCi HGNC:1317. GCFC2.
MIMi 189901. gene.
neXtProti NX_P16383.
PharmGKBi PA25892.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG294271.
GeneTreei ENSGT00390000000455.
HOGENOMi HOG000112699.
HOVERGENi HBG101878.
InParanoidi P16383.
KOi K09061.
OMAi QDTWEQQ.
OrthoDBi EOG79KPGP.
PhylomeDBi P16383.
TreeFami TF315109.

Miscellaneous databases

ChiTaRSi GCFC2. human.
GeneWikii C2orf3.
GenomeRNAii 6936.
NextBioi 27141.
PROi P16383.
SOURCEi Search...

Gene expression databases

Bgeei P16383.
CleanExi HS_C2orf3.
ExpressionAtlasi P16383. baseline and differential.
Genevestigatori P16383.

Family and domain databases

InterProi IPR012890. GCFC.
IPR022783. GCFC_dom.
[Graphical view ]
PANTHERi PTHR12214. PTHR12214. 1 hit.
Pfami PF07842. GCFC. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular cloning and characterization of a human DNA binding factor that represses transcription."
    Kageyama R., Pastan I.
    Cell 59:815-825(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
  2. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3).
  3. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
    Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
    , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
    Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], VARIANT ALA-32.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Skin.
  6. "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
    Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
    Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  7. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-16; SER-17; SER-19; THR-213; SER-214 AND SER-217, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  8. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
    Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
    Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
    Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
    Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-16; SER-17; SER-19; THR-213; SER-214 AND SER-217, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Leukemic T-cell.
  10. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
    Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
    Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-96 AND THR-97, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  11. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-16; SER-17; SER-19; SER-96 AND THR-97, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  13. "Identification of a novel component C2ORF3 in the lariat-intron complex: lack of C2ORF3 interferes with pre-mRNA splicing via intron turnover pathway."
    Yoshimoto R., Okawa K., Yoshida M., Ohno M., Kataoka N.
    Genes Cells 19:78-87(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, IDENTIFICATION IN THE INTRON LARGE COMPLEX, SUBCELLULAR LOCATION, INTERACTION WITH TFIP11 AND DHX15.

Entry informationi

Entry nameiGCFC2_HUMAN
AccessioniPrimary (citable) accession number: P16383
Secondary accession number(s): A4UHQ8
, O95032, Q53TY0, Q6P2F2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: November 28, 2006
Last modified: November 26, 2014
This is version 141 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

External Data

Dasty 3