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Protein

Pre-mRNA-splicing factor SYF1

Gene

XAB2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: 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

  • blastocyst development Source: Ensembl
  • cerebral cortex development Source: Ensembl
  • generation of catalytic spliceosome for first transesterification step Source: GO_Central
  • mRNA splicing, via spliceosome Source: UniProtKB
  • transcription, DNA-templated Source: UniProtKB
  • 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

BioCyciZFISH:ENSG00000076924-MONOMER.
ReactomeiR-HSA-6781823. Formation of TC-NER Pre-Incision Complex.
R-HSA-6781827. Transcription-Coupled Nucleotide Excision Repair (TC-NER).
R-HSA-6782135. Dual incision in TC-NER.
R-HSA-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-HSA-72163. mRNA Splicing - Major Pathway.

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
Proteomesi
  • UP000005640 Componenti: 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

  • catalytic step 1 spliceosome Source: GO_Central
  • catalytic step 2 spliceosome Source: UniProtKB
  • membrane Source: UniProtKB
  • nucleoplasm Source: Reactome
  • nucleus Source: UniProtKB
  • post-mRNA release spliceosomal complex Source: GO_Central
  • prespliceosome Source: GO_Central
  • Prp19 complex Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

DisGeNETi56949.
OpenTargetsiENSG00000076924.
PharmGKBiPA134905925.

Polymorphism and mutation databases

BioMutaiXAB2.
DMDMi25091548.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001064141 – 855Pre-mRNA-splicing factor SYF1Add BLAST855

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei420N6-acetyllysineCombined sources1
Modified residuei851PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ9HCS7.
MaxQBiQ9HCS7.
PaxDbiQ9HCS7.
PeptideAtlasiQ9HCS7.
PRIDEiQ9HCS7.

PTM databases

iPTMnetiQ9HCS7.
PhosphoSitePlusiQ9HCS7.

Expressioni

Gene expression databases

BgeeiENSG00000076924.
CleanExiHS_XAB2.
GenevisibleiQ9HCS7. HS.

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
ISY1Q9ULR06EBI-295232,EBI-2557660
POLR2AP249282EBI-295232,EBI-295301
PPIEQ9UNP98EBI-295232,EBI-591818
SF3B2Q134352EBI-295232,EBI-749111
SNW1Q135732EBI-295232,EBI-632715
XPAP230252EBI-295232,EBI-295222

Protein-protein interaction databases

BioGridi121273. 71 interactors.
DIPiDIP-31646N.
IntActiQ9HCS7. 28 interactors.
MINTiMINT-1475513.
STRINGi9606.ENSP00000351137.

Structurei

3D structure databases

ProteinModelPortaliQ9HCS7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati15 – 47HAT 1CuratedAdd BLAST33
Repeati48 – 80HAT 2CuratedAdd BLAST33
Repeati90 – 122HAT 3CuratedAdd BLAST33
Repeati124 – 158HAT 4CuratedAdd BLAST35
Repeati160 – 192HAT 5CuratedAdd BLAST33
Repeati198 – 230HAT 6Add BLAST33
Repeati235 – 268HAT 7Add BLAST34
Repeati270 – 305HAT 8Add BLAST36
Repeati369 – 407HAT 9Add BLAST39
Repeati498 – 530HAT 10Add BLAST33
Repeati532 – 566HAT 11Add BLAST35
Repeati571 – 605HAT 12Add BLAST35
Repeati643 – 677HAT 13Add BLAST35
Repeati679 – 713HAT 14Add BLAST35

Sequence similaritiesi

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

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG2047. Eukaryota.
ENOG410XPD9. LUCA.
GeneTreeiENSGT00550000075140.
HOGENOMiHOG000176133.
HOVERGENiHBG024066.
InParanoidiQ9HCS7.
KOiK12867.
OMAiARAIYVH.
OrthoDBiEOG091G01UP.
PhylomeDBiQ9HCS7.
TreeFamiTF300866.

Family and domain databases

Gene3Di1.25.40.10. 4 hits.
InterProiIPR003107. HAT.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical_dom.
IPR019734. TPR_repeat.
[Graphical view]
PfamiPF13181. TPR_8. 2 hits.
[Graphical view]
SMARTiSM00386. HAT. 11 hits.
SM00028. TPR. 3 hits.
[Graphical view]
SUPFAMiSSF48452. SSF48452. 4 hits.

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

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti68Y → T in AAF86951 (Ref. 2) Curated1
Sequence conflicti140L → M in BAB15807 (PubMed:10944529).Curated1
Sequence conflicti447E → K in AAH08778 (PubMed:15489334).Curated1
Sequence conflicti467A → V in AAF86951 (Ref. 2) Curated1
Sequence conflicti680E → K in AAF86951 (Ref. 2) Curated1
Sequence conflicti751 – 753SAT → IP in AAF86951 (Ref. 2) Curated3

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_016248126V → I.1 PublicationCorresponds to variant rs4134822dbSNPEnsembl.1
Natural variantiVAR_016249454R → Q.1 PublicationCorresponds to variant rs4134850dbSNPEnsembl.1
Natural variantiVAR_016250702A → T.1 PublicationCorresponds to variant rs4134865dbSNPEnsembl.1

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

EnsembliENST00000358368; ENSP00000351137; ENSG00000076924.
GeneIDi56949.
KEGGihsa:56949.
UCSCiuc002mgx.4. human.

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.
CCDSiCCDS32892.1.
RefSeqiNP_064581.2. NM_020196.2.
UniGeneiHs.9822.

3D structure databases

ProteinModelPortaliQ9HCS7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121273. 71 interactors.
DIPiDIP-31646N.
IntActiQ9HCS7. 28 interactors.
MINTiMINT-1475513.
STRINGi9606.ENSP00000351137.

PTM databases

iPTMnetiQ9HCS7.
PhosphoSitePlusiQ9HCS7.

Polymorphism and mutation databases

BioMutaiXAB2.
DMDMi25091548.

Proteomic databases

EPDiQ9HCS7.
MaxQBiQ9HCS7.
PaxDbiQ9HCS7.
PeptideAtlasiQ9HCS7.
PRIDEiQ9HCS7.

Protocols and materials databases

DNASUi56949.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000358368; ENSP00000351137; ENSG00000076924.
GeneIDi56949.
KEGGihsa:56949.
UCSCiuc002mgx.4. human.

Organism-specific databases

CTDi56949.
DisGeNETi56949.
GeneCardsiXAB2.
HGNCiHGNC:14089. XAB2.
MIMi610850. gene.
neXtProtiNX_Q9HCS7.
OpenTargetsiENSG00000076924.
PharmGKBiPA134905925.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2047. Eukaryota.
ENOG410XPD9. LUCA.
GeneTreeiENSGT00550000075140.
HOGENOMiHOG000176133.
HOVERGENiHBG024066.
InParanoidiQ9HCS7.
KOiK12867.
OMAiARAIYVH.
OrthoDBiEOG091G01UP.
PhylomeDBiQ9HCS7.
TreeFamiTF300866.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000076924-MONOMER.
ReactomeiR-HSA-6781823. Formation of TC-NER Pre-Incision Complex.
R-HSA-6781827. Transcription-Coupled Nucleotide Excision Repair (TC-NER).
R-HSA-6782135. Dual incision in TC-NER.
R-HSA-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-HSA-72163. mRNA Splicing - Major Pathway.

Miscellaneous databases

ChiTaRSiXAB2. human.
GeneWikiiXAB2.
GenomeRNAii56949.
PROiQ9HCS7.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000076924.
CleanExiHS_XAB2.
GenevisibleiQ9HCS7. HS.

Family and domain databases

Gene3Di1.25.40.10. 4 hits.
InterProiIPR003107. HAT.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical_dom.
IPR019734. TPR_repeat.
[Graphical view]
PfamiPF13181. TPR_8. 2 hits.
[Graphical view]
SMARTiSM00386. HAT. 11 hits.
SM00028. TPR. 3 hits.
[Graphical view]
SUPFAMiSSF48452. SSF48452. 4 hits.
ProtoNetiSearch...

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 30, 2016
This is version 159 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.