SubmitCancel

Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

Q9HCS7

- SYF1_HUMAN

UniProt

Q9HCS7 - SYF1_HUMAN

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Protein
Pre-mRNA-splicing factor SYF1
Gene
XAB2, HCNP, KIAA1177, SYF1, PP3898
Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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. DNA repair Source: Reactome
  2. blastocyst development Source: Ensembl
  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
Complete GO annotation...

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)
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. nucleoplasm Source: Reactome
  3. nucleus Source: UniProtKB
Complete GO annotation...

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 SYF1
PRO_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.

Family & Domainsi

Domains and Repeats

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

Sequence similaritiesi

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

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.

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 conflict

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

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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 135 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

Similar proteinsi