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Q9HCS7

- SYF1_HUMAN

UniProt

Q9HCS7 - SYF1_HUMAN

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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

Functioni

Involved in transcription-coupled repair (TCR), transcription and pre-mRNA splicing.2 Publications

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
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)Imported
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Unplaced

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
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 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

BgeeiQ9HCS7.
CleanExiHS_XAB2.
ExpressionAtlasiQ9HCS7. baseline and differential.
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. Component of the XAB2 complex, a multimeric protein complex composed of XAB2, PRPF19, AQR, ZNF830, ISY1, and PPIE.3 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. 38 interactions.
IntActiQ9HCS7. 20 interactions.
MINTiMINT-1475513.
STRINGi9606.ENSP00000351137.

Structurei

3D structure databases

ProteinModelPortaliQ9HCS7.
SMRiQ9HCS7. Positions 257-288, 369-427, 496-546.
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.
GeneTreeiENSGT00550000075140.
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_dom.
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

        10         20         30         40         50
MVVMARLSRP ERPDLVFEEE DLPYEEEIMR NQFSVKCWLR YIEFKQGAPK
60 70 80 90 100
PRLNQLYERA LKLLPCSYKL WYRYLKARRA QVKHRCVTDP AYEDVNNCHE
110 120 130 140 150
RAFVFMHKMP RLWLDYCQFL MDQGRVTHTR RTFDRALRAL PITQHSRIWP
160 170 180 190 200
LYLRFLRSHP LPETAVRGYR RFLKLSPESA EEYIEYLKSS DRLDEAAQRL
210 220 230 240 250
ATVVNDERFV SKAGKSNYQL WHELCDLISQ NPDKVQSLNV DAIIRGGLTR
260 270 280 290 300
FTDQLGKLWC SLADYYIRSG HFEKARDVYE EAIRTVMTVR DFTQVFDSYA
310 320 330 340 350
QFEESMIAAK METASELGRE EEDDVDLELR LARFEQLISR RPLLLNSVLL
360 370 380 390 400
RQNPHHVHEW HKRVALHQGR PREIINTYTE AVQTVDPFKA TGKPHTLWVA
410 420 430 440 450
FAKFYEDNGQ LDDARVILEK ATKVNFKQVD DLASVWCQCG ELELRHENYD
460 470 480 490 500
EALRLLRKAT ALPARRAEYF DGSEPVQNRV YKSLKVWSML ADLEESLGTF
510 520 530 540 550
QSTKAVYDRI LDLRIATPQI VINYAMFLEE HKYFEESFKA YERGISLFKW
560 570 580 590 600
PNVSDIWSTY LTKFIARYGG RKLERARDLF EQALDGCPPK YAKTLYLLYA
610 620 630 640 650
QLEEEWGLAR HAMAVYERAT RAVEPAQQYD MFNIYIKRAA EIYGVTHTRG
660 670 680 690 700
IYQKAIEVLS DEHAREMCLR FADMECKLGE IDRARAIYSF CSQICDPRTT
710 720 730 740 750
GAFWQTWKDF EVRHGNEDTI KEMLRIRRSV QATYNTQVNF MASQMLKVSG
760 770 780 790 800
SATGTVSDLA PGQSGMDDMK LLEQRAEQLA AEAERDQPLR AQSKILFVRS
810 820 830 840 850
DASREELAEL AQQVNPEEIQ LGEDEDEDEM DLEPNEVRLE QQSVPAAVFG

SLKED
Length:855
Mass (Da):100,010
Last modified:October 1, 2002 - v2
Checksum:iCF766917CD65F6FD
GO

Sequence cautioni

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

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:
EMBLi
GenBanki
DDBJi
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

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:
EMBLi
GenBanki
DDBJi
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 257-288, 369-427, 496-546.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 121273. 38 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

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.
GeneTreei ENSGT00550000075140.
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

Bgeei Q9HCS7.
CleanExi HS_XAB2.
ExpressionAtlasi Q9HCS7. baseline and differential.
Genevestigatori Q9HCS7.

Family and domain databases

Gene3Di 1.25.40.10. 4 hits.
InterProi IPR003107. HAT.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical_dom.
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. "Isolation of XAB2 complex involved in pre-mRNA splicing, transcription, and transcription-coupled repair."
    Kuraoka I., Ito S., Wada T., Hayashida M., Lee L., Saijo M., Nakatsu Y., Matsumoto M., Matsunaga T., Handa H., Qin J., Nakatani Y., Tanaka K.
    J. Biol. Chem. 283:940-950(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, IDENTIFICATION AS PART OF THE XAB2 COMPLEX.
  10. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-851, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  11. "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].
  12. 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: November 26, 2014
This is version 138 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