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Q9HCS7

- SYF1_HUMAN

UniProt

Q9HCS7 - SYF1_HUMAN

Protein

Pre-mRNA-splicing factor SYF1

Gene

XAB2

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 136 (01 Oct 2014)
      Sequence version 2 (01 Oct 2002)
      Previous versions | rss
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    Functioni

    Involved in transcription-coupled repair (TCR), transcription and pre-mRNA splicing.1 Publication

    GO - Molecular functioni

    1. protein binding Source: UniProtKB

    GO - Biological processi

    1. blastocyst development Source: Ensembl
    2. DNA repair Source: Reactome
    3. mRNA splicing, via spliceosome Source: UniProtKB
    4. nucleotide-excision repair Source: Reactome
    5. transcription, DNA-templated Source: UniProtKB
    6. transcription-coupled nucleotide-excision repair Source: UniProtKB

    Keywords - Biological processi

    DNA damage, DNA repair, mRNA processing, mRNA splicing, Transcription

    Enzyme and pathway databases

    ReactomeiREACT_1941. Formation of transcription-coupled NER (TC-NER) repair complex.
    REACT_2222. Dual incision reaction in TC-NER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pre-mRNA-splicing factor SYF1
    Alternative name(s):
    Protein HCNP
    XPA-binding protein 2
    Gene namesi
    Name:XAB2
    Synonyms:HCNP, KIAA1177, SYF1
    ORF Names:PP3898
    OrganismiHomo sapiens (Human)Imported
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 19

    Organism-specific databases

    HGNCiHGNC:14089. XAB2.

    Subcellular locationi

    Nucleus By similarity
    Note: Detected in the splicing complex carrying pre-mRNA.By similarity

    GO - Cellular componenti

    1. catalytic step 2 spliceosome Source: UniProtKB
    2. membrane Source: UniProtKB
    3. nucleoplasm Source: Reactome
    4. nucleus Source: UniProtKB

    Keywords - Cellular componenti

    Nucleus, Spliceosome

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA134905925.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 855855Pre-mRNA-splicing factor SYF1PRO_0000106414Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei420 – 4201N6-acetyllysine1 Publication
    Modified residuei851 – 8511Phosphoserine1 Publication

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    MaxQBiQ9HCS7.
    PaxDbiQ9HCS7.
    PeptideAtlasiQ9HCS7.
    PRIDEiQ9HCS7.

    PTM databases

    PhosphoSiteiQ9HCS7.

    Expressioni

    Gene expression databases

    ArrayExpressiQ9HCS7.
    BgeeiQ9HCS7.
    CleanExiHS_XAB2.
    GenevestigatoriQ9HCS7.

    Interactioni

    Subunit structurei

    Associates with RNA polymerase II, the TCR-specific proteins CKN1/CSA and ERCC6/CSB, and XPA. Identified in the spliceosome C complex.2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    DHX16O602312EBI-295232,EBI-311446
    ERCC8Q132163EBI-295232,EBI-295260
    IKQ131232EBI-295232,EBI-713456
    ISY1Q9ULR02EBI-295232,EBI-2557660
    POLR2AP249282EBI-295232,EBI-295301
    PPIEQ9UNP93EBI-295232,EBI-591818
    SF3B2Q134352EBI-295232,EBI-749111
    SNW1Q135732EBI-295232,EBI-632715
    XPAP230252EBI-295232,EBI-295222

    Protein-protein interaction databases

    BioGridi121273. 32 interactions.
    IntActiQ9HCS7. 20 interactions.
    MINTiMINT-1475513.
    STRINGi9606.ENSP00000351137.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9HCS7.
    SMRiQ9HCS7. Positions 258-284.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Repeati15 – 4733HAT 1CuratedAdd
    BLAST
    Repeati48 – 8033HAT 2CuratedAdd
    BLAST
    Repeati90 – 12233HAT 3CuratedAdd
    BLAST
    Repeati124 – 15835HAT 4CuratedAdd
    BLAST
    Repeati160 – 19233HAT 5CuratedAdd
    BLAST
    Repeati198 – 23033HAT 6Add
    BLAST
    Repeati235 – 26834HAT 7Add
    BLAST
    Repeati270 – 30536HAT 8Add
    BLAST
    Repeati369 – 40739HAT 9Add
    BLAST
    Repeati498 – 53033HAT 10Add
    BLAST
    Repeati532 – 56635HAT 11Add
    BLAST
    Repeati571 – 60535HAT 12Add
    BLAST
    Repeati643 – 67735HAT 13Add
    BLAST
    Repeati679 – 71335HAT 14Add
    BLAST

    Sequence similaritiesi

    Belongs to the crooked-neck family.Curated
    Contains 14 HAT repeats.Curated

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiNOG289100.
    HOGENOMiHOG000176133.
    HOVERGENiHBG024066.
    InParanoidiQ9HCS7.
    KOiK12867.
    OMAiPITQHNR.
    OrthoDBiEOG7RV9FD.
    PhylomeDBiQ9HCS7.
    TreeFamiTF300866.

    Family and domain databases

    Gene3Di1.25.40.10. 4 hits.
    InterProiIPR003107. HAT.
    IPR013026. TPR-contain_dom.
    IPR011990. TPR-like_helical.
    IPR013105. TPR_2.
    IPR019734. TPR_repeat.
    [Graphical view]
    PfamiPF07719. TPR_2. 2 hits.
    [Graphical view]
    SMARTiSM00386. HAT. 11 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9HCS7-1 [UniParc]FASTAAdd to Basket

    « Hide

    MVVMARLSRP ERPDLVFEEE DLPYEEEIMR NQFSVKCWLR YIEFKQGAPK    50
    PRLNQLYERA LKLLPCSYKL WYRYLKARRA QVKHRCVTDP AYEDVNNCHE 100
    RAFVFMHKMP RLWLDYCQFL MDQGRVTHTR RTFDRALRAL PITQHSRIWP 150
    LYLRFLRSHP LPETAVRGYR RFLKLSPESA EEYIEYLKSS DRLDEAAQRL 200
    ATVVNDERFV SKAGKSNYQL WHELCDLISQ NPDKVQSLNV DAIIRGGLTR 250
    FTDQLGKLWC SLADYYIRSG HFEKARDVYE EAIRTVMTVR DFTQVFDSYA 300
    QFEESMIAAK METASELGRE EEDDVDLELR LARFEQLISR RPLLLNSVLL 350
    RQNPHHVHEW HKRVALHQGR PREIINTYTE AVQTVDPFKA TGKPHTLWVA 400
    FAKFYEDNGQ LDDARVILEK ATKVNFKQVD DLASVWCQCG ELELRHENYD 450
    EALRLLRKAT ALPARRAEYF DGSEPVQNRV YKSLKVWSML ADLEESLGTF 500
    QSTKAVYDRI LDLRIATPQI VINYAMFLEE HKYFEESFKA YERGISLFKW 550
    PNVSDIWSTY LTKFIARYGG RKLERARDLF EQALDGCPPK YAKTLYLLYA 600
    QLEEEWGLAR HAMAVYERAT RAVEPAQQYD MFNIYIKRAA EIYGVTHTRG 650
    IYQKAIEVLS DEHAREMCLR FADMECKLGE IDRARAIYSF CSQICDPRTT 700
    GAFWQTWKDF EVRHGNEDTI KEMLRIRRSV QATYNTQVNF MASQMLKVSG 750
    SATGTVSDLA PGQSGMDDMK LLEQRAEQLA AEAERDQPLR AQSKILFVRS 800
    DASREELAEL AQQVNPEEIQ LGEDEDEDEM DLEPNEVRLE QQSVPAAVFG 850
    SLKED 855
    Length:855
    Mass (Da):100,010
    Last modified:October 1, 2002 - v2
    Checksum:iCF766917CD65F6FD
    GO

    Sequence cautioni

    The sequence BAB84861.1 differs from that shown. Reason: Alternative splicing. Incomplete sequence.
    The sequence AAF86951.1 differs from that shown. Reason: Frameshift at positions 314, 411, 426, 429 and 468.
    The sequence AAH08778.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti68 – 681Y → T in AAF86951. 1 PublicationCurated
    Sequence conflicti140 – 1401L → M in BAB15807. (PubMed:10944529)Curated
    Sequence conflicti447 – 4471E → K in AAH08778. (PubMed:15489334)Curated
    Sequence conflicti467 – 4671A → V in AAF86951. 1 PublicationCurated
    Sequence conflicti680 – 6801E → K in AAF86951. 1 PublicationCurated
    Sequence conflicti751 – 7533SAT → IP in AAF86951. 1 PublicationCurated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti126 – 1261V → I.1 Publication
    Corresponds to variant rs4134822 [ dbSNP | Ensembl ].
    VAR_016248
    Natural varianti454 – 4541R → Q.1 Publication
    Corresponds to variant rs4134850 [ dbSNP | Ensembl ].
    VAR_016249
    Natural varianti702 – 7021A → T.1 Publication
    Corresponds to variant rs4134865 [ dbSNP | Ensembl ].
    VAR_016250

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB026111 mRNA. Translation: BAB15807.1.
    AF226051 mRNA. Translation: AAF86951.1. Frameshift.
    AF258567 mRNA. Translation: AAG23770.1.
    AF547265 Genomic DNA. Translation: AAN17847.1.
    BC007208 mRNA. Translation: AAH07208.1.
    BC008778 mRNA. Translation: AAH08778.1. Different initiation.
    AK074035 mRNA. Translation: BAB84861.1. Sequence problems.
    AB033003 mRNA. Translation: BAA86491.1.
    CCDSiCCDS32892.1.
    RefSeqiNP_064581.2. NM_020196.2.
    UniGeneiHs.9822.

    Genome annotation databases

    EnsembliENST00000358368; ENSP00000351137; ENSG00000076924.
    GeneIDi56949.
    KEGGihsa:56949.
    UCSCiuc002mgx.3. human.

    Polymorphism databases

    DMDMi25091548.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Web resourcesi

    NIEHS-SNPs

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB026111 mRNA. Translation: BAB15807.1 .
    AF226051 mRNA. Translation: AAF86951.1 . Frameshift.
    AF258567 mRNA. Translation: AAG23770.1 .
    AF547265 Genomic DNA. Translation: AAN17847.1 .
    BC007208 mRNA. Translation: AAH07208.1 .
    BC008778 mRNA. Translation: AAH08778.1 . Different initiation.
    AK074035 mRNA. Translation: BAB84861.1 . Sequence problems.
    AB033003 mRNA. Translation: BAA86491.1 .
    CCDSi CCDS32892.1.
    RefSeqi NP_064581.2. NM_020196.2.
    UniGenei Hs.9822.

    3D structure databases

    ProteinModelPortali Q9HCS7.
    SMRi Q9HCS7. Positions 258-284.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 121273. 32 interactions.
    IntActi Q9HCS7. 20 interactions.
    MINTi MINT-1475513.
    STRINGi 9606.ENSP00000351137.

    PTM databases

    PhosphoSitei Q9HCS7.

    Polymorphism databases

    DMDMi 25091548.

    Proteomic databases

    MaxQBi Q9HCS7.
    PaxDbi Q9HCS7.
    PeptideAtlasi Q9HCS7.
    PRIDEi Q9HCS7.

    Protocols and materials databases

    DNASUi 56949.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000358368 ; ENSP00000351137 ; ENSG00000076924 .
    GeneIDi 56949.
    KEGGi hsa:56949.
    UCSCi uc002mgx.3. human.

    Organism-specific databases

    CTDi 56949.
    GeneCardsi GC19M007684.
    HGNCi HGNC:14089. XAB2.
    MIMi 610850. gene.
    neXtProti NX_Q9HCS7.
    PharmGKBi PA134905925.
    HUGEi Search...
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG289100.
    HOGENOMi HOG000176133.
    HOVERGENi HBG024066.
    InParanoidi Q9HCS7.
    KOi K12867.
    OMAi PITQHNR.
    OrthoDBi EOG7RV9FD.
    PhylomeDBi Q9HCS7.
    TreeFami TF300866.

    Enzyme and pathway databases

    Reactomei REACT_1941. Formation of transcription-coupled NER (TC-NER) repair complex.
    REACT_2222. Dual incision reaction in TC-NER.

    Miscellaneous databases

    ChiTaRSi XAB2. human.
    GeneWikii XAB2.
    GenomeRNAii 56949.
    NextBioi 62545.
    PROi Q9HCS7.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9HCS7.
    Bgeei Q9HCS7.
    CleanExi HS_XAB2.
    Genevestigatori Q9HCS7.

    Family and domain databases

    Gene3Di 1.25.40.10. 4 hits.
    InterProi IPR003107. HAT.
    IPR013026. TPR-contain_dom.
    IPR011990. TPR-like_helical.
    IPR013105. TPR_2.
    IPR019734. TPR_repeat.
    [Graphical view ]
    Pfami PF07719. TPR_2. 2 hits.
    [Graphical view ]
    SMARTi SM00386. HAT. 11 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "XAB2, a novel tetratricopeptide repeat protein, involved in transcription-coupled DNA repair and transcription."
      Nakatsu Y., Asahina H., Citterio E., Rademakers S., Vermeulen W., Kamiuchi S., Yeo J.-P., Khaw M.-C., Saijo M., Kodo N., Matsuda T., Hoeijmakers J.H.J., Tanaka K.
      J. Biol. Chem. 275:34931-34937(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, SUBUNIT.
    2. "A novel gene expressed in human adrenal gland."
      Li Y., Wu T., Xu S., Ren S., Chen Z., Han Z.
      Submitted (JAN-2000) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Adrenal gland.
    3. "Large-scale cDNA transfection screening for genes related to cancer development and progression."
      Wan D., Gong Y., Qin W., Zhang P., Li J., Wei L., Zhou X., Li H., Qiu X., Zhong F., He L., Yu J., Yao G., Jiang H., Qian L., Yu Y., Shu H., Chen X.
      , Xu H., Guo M., Pan Z., Chen Y., Ge C., Yang S., Gu J.
      Proc. Natl. Acad. Sci. U.S.A. 101:15724-15729(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    4. NIEHS SNPs program
      Submitted (SEP-2002) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANTS ILE-126; GLN-454 AND THR-702.
    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].
      Tissue: Lung.
    6. "The nucleotide sequence of a long cDNA clone isolated from human spleen."
      Ohara O., Nagase T., Kikuno R., Okumura K.
      Submitted (JAN-2002) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 28-855.
      Tissue: Spleen.
    7. "Characterization of cDNA clones selected by the GeneMark analysis from size-fractionated cDNA libraries from human brain."
      Hirosawa M., Nagase T., Ishikawa K., Kikuno R., Nomura N., Ohara O.
      DNA Res. 6:329-336(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 101-855.
      Tissue: Brain.
    8. "Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis."
      Jurica M.S., Licklider L.J., Gygi S.P., Grigorieff N., Moore M.J.
      RNA 8:426-439(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE SPLICEOSOMAL C COMPLEX.
    9. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-851, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    10. "Lysine acetylation targets protein complexes and co-regulates major cellular functions."
      Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
      Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-420, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    11. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiSYF1_HUMAN
    AccessioniPrimary (citable) accession number: Q9HCS7
    Secondary accession number(s): Q8TET6
    , Q96HB0, Q96IW0, Q9NRG6, Q9ULP3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 15, 2002
    Last sequence update: October 1, 2002
    Last modified: October 1, 2014
    This is version 136 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 19
      Human chromosome 19: 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