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Q9HCS7 (SYF1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 134. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Pre-mRNA-splicing factor SYF1
Alternative name(s):
Protein HCNP
XPA-binding protein 2
Gene names
Name:XAB2
Synonyms:HCNP, KIAA1177, SYF1
ORF Names:PP3898
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length855 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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

Subunit structure

Associates with RNA polymerase II, the TCR-specific proteins CKN1/CSA and ERCC6/CSB, and XPA. Identified in the spliceosome C complex. Ref.1 Ref.8

Subcellular location

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

Sequence similarities

Belongs to the crooked-neck family.

Contains 14 HAT repeats.

Sequence caution

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.

The sequence BAB84861.1 differs from that shown. Reason: Alternative splicing. Incomplete sequence.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 855855Pre-mRNA-splicing factor SYF1
PRO_0000106414

Regions

Repeat15 – 4733HAT 1
Repeat48 – 8033HAT 2
Repeat90 – 12233HAT 3
Repeat124 – 15835HAT 4
Repeat160 – 19233HAT 5
Repeat198 – 23033HAT 6
Repeat235 – 26834HAT 7
Repeat270 – 30536HAT 8
Repeat369 – 40739HAT 9
Repeat498 – 53033HAT 10
Repeat532 – 56635HAT 11
Repeat571 – 60535HAT 12
Repeat643 – 67735HAT 13
Repeat679 – 71335HAT 14

Amino acid modifications

Modified residue4201N6-acetyllysine Ref.10
Modified residue8511Phosphoserine Ref.9

Natural variations

Natural variant1261V → I. Ref.4
Corresponds to variant rs4134822 [ dbSNP | Ensembl ].
VAR_016248
Natural variant4541R → Q. Ref.4
Corresponds to variant rs4134850 [ dbSNP | Ensembl ].
VAR_016249
Natural variant7021A → T. Ref.4
Corresponds to variant rs4134865 [ dbSNP | Ensembl ].
VAR_016250

Experimental info

Sequence conflict681Y → T in AAF86951. Ref.2
Sequence conflict1401L → M in BAB15807. Ref.1
Sequence conflict4471E → K in AAH08778. Ref.5
Sequence conflict4671A → V in AAF86951. Ref.2
Sequence conflict6801E → K in AAF86951. Ref.2
Sequence conflict751 – 7533SAT → IP in AAF86951. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Q9HCS7 [UniParc].

Last modified October 1, 2002. Version 2.
Checksum: CF766917CD65F6FD

FASTA855100,010
        10         20         30         40         50         60 
MVVMARLSRP ERPDLVFEEE DLPYEEEIMR NQFSVKCWLR YIEFKQGAPK PRLNQLYERA 

        70         80         90        100        110        120 
LKLLPCSYKL WYRYLKARRA QVKHRCVTDP AYEDVNNCHE RAFVFMHKMP RLWLDYCQFL 

       130        140        150        160        170        180 
MDQGRVTHTR RTFDRALRAL PITQHSRIWP LYLRFLRSHP LPETAVRGYR RFLKLSPESA 

       190        200        210        220        230        240 
EEYIEYLKSS DRLDEAAQRL ATVVNDERFV SKAGKSNYQL WHELCDLISQ NPDKVQSLNV 

       250        260        270        280        290        300 
DAIIRGGLTR FTDQLGKLWC SLADYYIRSG HFEKARDVYE EAIRTVMTVR DFTQVFDSYA 

       310        320        330        340        350        360 
QFEESMIAAK METASELGRE EEDDVDLELR LARFEQLISR RPLLLNSVLL RQNPHHVHEW 

       370        380        390        400        410        420 
HKRVALHQGR PREIINTYTE AVQTVDPFKA TGKPHTLWVA FAKFYEDNGQ LDDARVILEK 

       430        440        450        460        470        480 
ATKVNFKQVD DLASVWCQCG ELELRHENYD EALRLLRKAT ALPARRAEYF DGSEPVQNRV 

       490        500        510        520        530        540 
YKSLKVWSML ADLEESLGTF QSTKAVYDRI LDLRIATPQI VINYAMFLEE HKYFEESFKA 

       550        560        570        580        590        600 
YERGISLFKW PNVSDIWSTY LTKFIARYGG RKLERARDLF EQALDGCPPK YAKTLYLLYA 

       610        620        630        640        650        660 
QLEEEWGLAR HAMAVYERAT RAVEPAQQYD MFNIYIKRAA EIYGVTHTRG IYQKAIEVLS 

       670        680        690        700        710        720 
DEHAREMCLR FADMECKLGE IDRARAIYSF CSQICDPRTT GAFWQTWKDF EVRHGNEDTI 

       730        740        750        760        770        780 
KEMLRIRRSV QATYNTQVNF MASQMLKVSG SATGTVSDLA PGQSGMDDMK LLEQRAEQLA 

       790        800        810        820        830        840 
AEAERDQPLR AQSKILFVRS DASREELAEL AQQVNPEEIQ LGEDEDEDEM DLEPNEVRLE 

       850 
QQSVPAAVFG SLKED 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
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]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Web resources

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS32892.1.
RefSeqNP_064581.2. NM_020196.2.
UniGeneHs.9822.

3D structure databases

ProteinModelPortalQ9HCS7.
SMRQ9HCS7. Positions 258-284.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid121273. 32 interactions.
IntActQ9HCS7. 20 interactions.
MINTMINT-1475513.
STRING9606.ENSP00000351137.

PTM databases

PhosphoSiteQ9HCS7.

Polymorphism databases

DMDM25091548.

Proteomic databases

MaxQBQ9HCS7.
PaxDbQ9HCS7.
PeptideAtlasQ9HCS7.
PRIDEQ9HCS7.

Protocols and materials databases

DNASU56949.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000358368; ENSP00000351137; ENSG00000076924.
GeneID56949.
KEGGhsa:56949.
UCSCuc002mgx.3. human.

Organism-specific databases

CTD56949.
GeneCardsGC19M007684.
HGNCHGNC:14089. XAB2.
MIM610850. gene.
neXtProtNX_Q9HCS7.
PharmGKBPA134905925.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG289100.
HOGENOMHOG000176133.
HOVERGENHBG024066.
InParanoidQ9HCS7.
KOK12867.
OMAPITQHNR.
OrthoDBEOG7RV9FD.
PhylomeDBQ9HCS7.
TreeFamTF300866.

Enzyme and pathway databases

ReactomeREACT_216. DNA Repair.

Gene expression databases

ArrayExpressQ9HCS7.
BgeeQ9HCS7.
CleanExHS_XAB2.
GenevestigatorQ9HCS7.

Family and domain databases

Gene3D1.25.40.10. 4 hits.
InterProIPR003107. HAT.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical.
IPR013105. TPR_2.
IPR019734. TPR_repeat.
[Graphical view]
PfamPF07719. TPR_2. 2 hits.
[Graphical view]
SMARTSM00386. HAT. 11 hits.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSXAB2. human.
GeneWikiXAB2.
GenomeRNAi56949.
NextBio62545.
PROQ9HCS7.
SOURCESearch...

Entry information

Entry nameSYF1_HUMAN
AccessionPrimary (citable) accession number: Q9HCS7
Secondary accession number(s): Q8TET6 expand/collapse secondary AC list , Q96HB0, Q96IW0, Q9NRG6, Q9ULP3
Entry history
Integrated into UniProtKB/Swiss-Prot: November 15, 2002
Last sequence update: October 1, 2002
Last modified: July 9, 2014
This is version 134 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 19

Human chromosome 19: entries, gene names and cross-references to MIM