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P16383

- GCFC2_HUMAN

UniProt

P16383 - GCFC2_HUMAN

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
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    • History
      Entry version 139 (01 Oct 2014)
      Sequence version 2 (28 Nov 2006)
      Previous versions | rss
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    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

    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. nucleoplasm Source: UniProtKB-SubCell
    3. nucleus Source: UniProtKB
    4. U2-type post-mRNA release spliceosomal complex Source: UniProtKB

    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

    ArrayExpressiP16383.
    BgeeiP16383.
    CleanExiHS_C2orf3.
    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. 4 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.
    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

    MAHRPKRTFR QRAADSSDSD GAEESPAEPG APRELPVPGS AEEEPPSGGG    50
    RAQVAGLPHR VRGPRGRGRV WASSRRATKA APRADEGSES RTLDVSTDEE 100
    DKIHHSSESK DDQGLSSDSS SSLGEKELSS TVKIPDAAFI QAARRKRELA 150
    RAQDDYISLD VQHTSSISGM KRESEDDPES EPDDHEKRIP FTLRPQTLRQ 200
    RMAEESISRN EETSEESQED EKQDTWEQQQ MRKAVKIIEE RDIDLSCGNG 250
    SSKVKKFDTS ISFPPVNLEI IKKQLNTRLT LLQETHRSHL REYEKYVQDV 300
    KSSKSTIQNL ESSSNQALNC KFYKSMKIYV ENLIDCLNEK IINIQEIESS 350
    MHALLLKQAM TFMKRRQDEL KHESTYLQQL SRKDETSTSG NFSVDEKTQW 400
    ILEEIESRRT KRRQARVLSG NCNHQEGTSS DDELPSAEMI DFQKSQGDIL 450
    QKQKKVFEEV QDDFCNIQNI LLKFQQWREK FPDSYYEAFI SLCIPKLLNP 500
    LIRVQLIDWN PLKLESTGLK EMPWFKSVEE FMDSSVEDSK KESSSDKKVL 550
    SAIINKTIIP RLTDFVEFLW DPLSTSQTTS LITHCRVILE EHSTCENEVS 600
    KSRQDLLKSI VSRMKKAVED DVFIPLYPKS AVENKTSPHS KFQERQFWSG 650
    LKLFRNILLW NGLLTDDTLQ ELGLGKLLNR YLIIALLNAT PGPDVVKKCN 700
    QVAACLPEKW FENSAMRTSI PQLENFIQFL LQSAHKLSRS EFRDEVEEII 750
    LILVKIKALN QAESFIGEHH LDHLKSLIKE D 781
    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.
    The sequence AAA35598.1 differs from that shown. Reason: Frameshift at position 147.

    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:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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. 4 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.
    HOGENOMi HOG000112699.
    HOVERGENi HBG101878.
    InParanoidi P16383.
    KOi K09061.
    OMAi QDTWEQQ.
    OrthoDBi EOG79KPGP.
    PhylomeDBi P16383.
    TreeFami TF315109.

    Miscellaneous databases

    GeneWikii C2orf3.
    GenomeRNAii 6936.
    NextBioi 27141.
    PROi P16383.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi P16383.
    Bgeei P16383.
    CleanExi HS_C2orf3.
    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

    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: October 1, 2014
    This is version 139 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