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Aliases for XAB2 Gene

Aliases for XAB2 Gene

  • XPA Binding Protein 2 2 3
  • SYF1 Pre-MRNA-Splicing Factor 2 3
  • XPA-Binding Protein 2 3 4
  • HCNP 3 4
  • SYF1 3 4
  • RNA Splicing Factor (S. Cerevisiae) 2
  • SYF1 Homolog, RNA Splicing Factor 3
  • Pre-MRNA-Splicing Factor SYF1 3
  • Crn-Related Protein Kim1 3
  • SYF1 Homolog 2
  • Protein HCNP 4
  • KIAA1177 4
  • NTC90 3
  • HCRN 3

External Ids for XAB2 Gene

Summaries for XAB2 Gene

GeneCards Summary for XAB2 Gene

XAB2 (XPA Binding Protein 2) is a Protein Coding gene. Among its related pathways are Chks in Checkpoint Regulation and DNA Repair.

UniProtKB/Swiss-Prot for XAB2 Gene

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

Gene Wiki entry for XAB2 Gene

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for XAB2 Gene

Genomics for XAB2 Gene

Genomic Location for XAB2 Gene

Start:
7,619,525 bp from pter
End:
7,629,565 bp from pter
Size:
10,041 bases
Orientation:
Minus strand

Genomic View for XAB2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for XAB2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for XAB2 Gene

Regulatory Elements for XAB2 Gene

Proteins for XAB2 Gene

  • Protein details for XAB2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HCS7-SYF1_HUMAN
    Recommended name:
    Pre-mRNA-splicing factor SYF1
    Protein Accession:
    Q9HCS7
    Secondary Accessions:
    • Q8TET6
    • Q96HB0
    • Q96IW0
    • Q9NRG6
    • Q9ULP3

    Protein attributes for XAB2 Gene

    Size:
    855 amino acids
    Molecular mass:
    100010 Da
    Quaternary structure:
    • 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.
    SequenceCaution:
    • Sequence=AAF86951.1; Type=Frameshift; Positions=314, 411, 426, 429, 468; Evidence={ECO:0000305}; Sequence=AAH08778.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAB84861.1; Type=Miscellaneous discrepancy; Note=Alternative splicing. Incomplete sequence.; Evidence={ECO:0000305};

neXtProt entry for XAB2 Gene

Proteomics data for XAB2 Gene at MOPED

Post-translational modifications for XAB2 Gene

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys174, Lys637, Lys654, Lys677, and Lys708

Other Protein References for XAB2 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for XAB2 Gene

Domains for XAB2 Gene

Protein Domains for XAB2 Gene

UniProtKB/Swiss-Prot:

SYF1_HUMAN
Family:
  • Belongs to the crooked-neck family.:
    • Q9HCS7
Similarity:
  • Contains 14 HAT repeats.:
    • Q9HCS7
genes like me logo Genes that share domains with XAB2: view

No data available for Gene Families for XAB2 Gene

Function for XAB2 Gene

Molecular function for XAB2 Gene

UniProtKB/Swiss-Prot Function: Involved in transcription-coupled repair (TCR), transcription and pre-mRNA splicing.

Gene Ontology (GO) - Molecular Function for XAB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 10944529
genes like me logo Genes that share ontologies with XAB2: view
genes like me logo Genes that share phenotypes with XAB2: view

Animal Models for XAB2 Gene

MGI Knock Outs for XAB2:

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for XAB2 Gene

Localization for XAB2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for XAB2 Gene

Nucleus. Note=Detected in the splicing complex carrying pre-mRNA. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for XAB2 Gene COMPARTMENTS Subcellular localization image for XAB2 gene
Compartment Confidence
nucleus 5
cytosol 3
extracellular 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for XAB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular --
GO:0005634 nucleus IC 10944529
GO:0005654 nucleoplasm TAS --
GO:0016020 membrane IDA 19946888
GO:0071013 catalytic step 2 spliceosome IDA 11991638
genes like me logo Genes that share ontologies with XAB2: view

Pathways for XAB2 Gene

genes like me logo Genes that share pathways with XAB2: view

Pathways by source for XAB2 Gene

Gene Ontology (GO) - Biological Process for XAB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome IC 11991638
GO:0001824 blastocyst development IEA --
GO:0006281 DNA repair TAS --
GO:0006283 transcription-coupled nucleotide-excision repair TAS --
GO:0006289 nucleotide-excision repair TAS --
genes like me logo Genes that share ontologies with XAB2: view

Transcripts for XAB2 Gene

mRNA/cDNA for XAB2 Gene

Unigene Clusters for XAB2 Gene

XPA binding protein 2:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for XAB2 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15a · 15b ^ 16 ^ 17 ^ 18 ^ 19a · 19b
SP1: -
SP2:
SP3:
SP4:

Relevant External Links for XAB2 Gene

GeneLoc Exon Structure for
XAB2
ECgene alternative splicing isoforms for
XAB2

Expression for XAB2 Gene

mRNA expression in normal human tissues for XAB2 Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for XAB2 Gene

SOURCE GeneReport for Unigene cluster for XAB2 Gene Hs.9822

genes like me logo Genes that share expressions with XAB2: view

Orthologs for XAB2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for XAB2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia XAB2 36
  • 99.08 (n)
  • 100 (a)
XAB2 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia XAB2 36
  • 91.5 (n)
  • 98.95 (a)
XAB2 37
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia XAB2 36
  • 90.72 (n)
  • 98.83 (a)
XAB2 37
  • 99 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Xab2 36
  • 89.04 (n)
  • 98.83 (a)
Xab2 16
Xab2 37
  • 99 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia XAB2 37
  • 90 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 37
  • 74 (a)
OneToMany
-- 37
  • 86 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Xab2 36
  • 89.55 (n)
  • 98.95 (a)
lizard
(Anolis carolinensis)
Reptilia XAB2 37
  • 78 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.1969 36
tropical clawed frog
(Silurana tropicalis)
Amphibia xab2 36
  • 70.77 (n)
  • 76.46 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4228 36
zebrafish
(Danio rerio)
Actinopterygii xab2 36
  • 74.18 (n)
  • 81.85 (a)
xab2 37
  • 81 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012369 36
  • 70.75 (n)
  • 64.75 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG6197 36
  • 64.44 (n)
  • 63.63 (a)
CG6197 37
  • 60 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea C50F2.3 36
  • 53.65 (n)
  • 49.88 (a)
C50F2.3 37
  • 48 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SYF1 37
  • 22 (a)
OneToOne
SYF1 39
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G28740 36
  • 55.39 (n)
  • 53.62 (a)
rice
(Oryza sativa)
Liliopsida Os.33176 36
Os07g0644300 36
  • 57.35 (n)
  • 52.87 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU08036 36
  • 59.44 (n)
  • 54.16 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes cwf3 36
  • 49.45 (n)
  • 45.6 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.6158 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 65 (a)
OneToOne
Species with no ortholog for XAB2:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for XAB2 Gene

ENSEMBL:
Gene Tree for XAB2 (if available)
TreeFam:
Gene Tree for XAB2 (if available)

Paralogs for XAB2 Gene

Selected SIMAP similar genes for XAB2 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with XAB2: view

No data available for Paralogs for XAB2 Gene

Variants for XAB2 Gene

Sequence variations from dbSNP and Humsavar for XAB2 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type MAF
rs732457 -- 7,623,952(-) GGGAG(C/T)GGAGG intron-variant
rs794078 -- 7,620,957(+) GCCCT(A/G)GTGGC reference, synonymous-codon
rs794079 -- 7,621,876(+) TAGGA(C/T)TCTGT intron-variant
rs794080 -- 7,623,912(+) AGGGG(C/T)GGAGA intron-variant
rs794081 -- 7,625,798(+) TTCTG(C/T)CTGTG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for XAB2 Gene

Variant ID Type Subtype PubMed ID
esv2751809 CNV Gain 17911159
nsv833730 CNV Loss 17160897
dgv3712n71 CNV Loss 21882294
nsv910970 CNV Loss 21882294
nsv833731 CNV Loss 17160897
nsv910979 CNV Loss 21882294
esv993190 CNV Deletion 20482838

Relevant External Links for XAB2 Gene

HapMap Linkage Disequilibrium report
XAB2

Disorders for XAB2 Gene

(2) University of Copenhagen DISEASES for XAB2 Gene

Relevant External Links for XAB2

Genetic Association Database (GAD)
XAB2
Human Genome Epidemiology (HuGE) Navigator
XAB2
genes like me logo Genes that share disorders with XAB2: view

No data available for UniProtKB/Swiss-Prot for XAB2 Gene

Publications for XAB2 Gene

  1. XAB2, a novel tetratricopeptide repeat protein, involved in transcription-coupled DNA repair and transcription. (PMID: 10944529) Nakatsu Y. … Tanaka K. (J. Biol. Chem. 2000) 2 3 4 23
  2. Isolation of XAB2 complex involved in pre-mRNA splicing, transcription, and transcription-coupled repair. (PMID: 17981804) Kuraoka I. … Tanaka K. (J. Biol. Chem. 2008) 3 4 23
  3. Characterization of cDNA clones selected by the GeneMark analysis from size-fractionated cDNA libraries from human brain. (PMID: 10574461) Hirosawa M. … Ohara O. (DNA Res. 1999) 3 4
  4. Cockayne syndrome A and B proteins differentially regulate recruitment of chromatin remodeling and repair factors to stalled RNA polymerase II in vivo. (PMID: 16916636) Fousteri M. … Mullenders L.H. (Mol. Cell 2006) 3 23
  5. Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. (PMID: 11991638) Jurica M.S. … Moore M.J. (RNA 2002) 3 4

Products for XAB2 Gene

Sources for XAB2 Gene

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