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Protein

Pre-mRNA-splicing factor SYF1

Gene

XAB2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11991638, PubMed:28502770, PubMed:28076346). Involved in transcription-coupled repair (TCR), transcription and pre-mRNA splicing (PubMed:10944529, PubMed:17981804).5 Publications

GO - Biological processi

Keywordsi

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

Enzyme and pathway databases

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

EuPathDBiHostDB:ENSG00000076924.11
HGNCiHGNC:14089 XAB2
MIMi610850 gene
neXtProtiNX_Q9HCS7

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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
ProteomicsDBi81796

PTM databases

iPTMnetiQ9HCS7
PhosphoSitePlusiQ9HCS7

Expressioni

Gene expression databases

BgeeiENSG00000076924
CleanExiHS_XAB2
GenevisibleiQ9HCS7 HS

Organism-specific databases

HPAiHPA048751

Interactioni

Subunit structurei

Associates with RNA polymerase II, the TCR-specific proteins CKN1/CSA and ERCC6/CSB, and XPA (PubMed:10944529). Identified in the spliceosome C complex (PubMed:11991638, PubMed:28502770, PubMed:28076346). Component of the XAB2 complex, a multimeric protein complex composed of XAB2, PRPF19, AQR, ZNF830, ISY1, and PPIE (PubMed:17981804). Identified in a pentameric intron-binding (IB) complex composed of AQR, XAB2, ISY1, ZNF830 and PPIE that is incorporated into the spliceosome as a preassembled complex (PubMed:25599396). The IB complex does not contain PRPF19 (PubMed:25599396).6 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi121273, 85 interactors
CORUMiQ9HCS7
DIPiDIP-31646N
IntActiQ9HCS7, 33 interactors
MINTiQ9HCS7
STRINGi9606.ENSP00000351137

Structurei

3D structure databases

ProteinModelPortaliQ9HCS7
SMRiQ9HCS7
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

Keywords - Domaini

Repeat

Phylogenomic databases

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

Family and domain databases

Gene3Di1.25.40.10, 3 hits
InterProiView protein in InterPro
IPR003107 HAT
IPR013026 TPR-contain_dom
IPR011990 TPR-like_helical_dom_sf
IPR019734 TPR_repeat
PfamiView protein in Pfam
PF13181 TPR_8, 2 hits
SMARTiView protein in SMART
SM00386 HAT, 11 hits
SM00028 TPR, 3 hits
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 → I1 PublicationCorresponds to variant dbSNP:rs4134822Ensembl.1
Natural variantiVAR_016249454R → Q1 PublicationCorresponds to variant dbSNP:rs4134850Ensembl.1
Natural variantiVAR_016250702A → T1 PublicationCorresponds to variant dbSNP:rs4134865Ensembl.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

Similar proteinsi

Entry informationi

Entry nameiSYF1_HUMAN
AccessioniPrimary (citable) accession number: Q9HCS7
Secondary accession number(s): Q8TET6
, Q96HB0, Q96IW0, Q9NRG6, Q9ULP3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 15, 2002
Last sequence update: October 1, 2002
Last modified: July 18, 2018
This is version 175 of the entry and version 2 of the sequence. See 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

3D-structure, 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

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