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Aliases for XAB2 Gene

Aliases for XAB2 Gene

  • XPA Binding Protein 2 2 3 5
  • 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
  • Crn-Related Protein Kim1 3
  • SYF1 Homolog 2
  • Protein HCNP 4
  • KIAA1177 4
  • NTC90 3
  • HCRN 3

External Ids for XAB2 Gene

Previous GeneCards Identifiers for XAB2 Gene

  • GC00U913006
  • GC19M007590
  • GC19M007354
  • GC19M007684

Summaries for XAB2 Gene

GeneCards Summary for XAB2 Gene

XAB2 (XPA Binding Protein 2) is a Protein Coding gene. Diseases associated with XAB2 include cockayne syndrome. Among its related pathways are DNA Double-Strand Break Repair and mRNA Splicing - Major Pathway.

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

Regulatory Elements for XAB2 Gene

Promoters for XAB2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around XAB2 on UCSC Golden Path with GeneCards custom track

Genomic Location for XAB2 Gene

Chromosome:
19
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

Genes around XAB2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
XAB2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for XAB2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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

  • Ubiquitination at Lys 174, Lys 637, Lys 654, Lys 677, and Lys 708
  • Modification sites at PhosphoSitePlus

Other Protein References for XAB2 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for XAB2 Gene

Domains & Families for XAB2 Gene

Protein Domains for XAB2 Gene

Suggested Antigen Peptide Sequences for XAB2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9HCS7

UniProtKB/Swiss-Prot:

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

Animal Models for XAB2 Gene

MGI Knock Outs for XAB2:

Animal Model Products

miRNA for XAB2 Gene

miRTarBase miRNAs that target XAB2

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets 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:0005654 nucleoplasm TAS --
GO:0016020 membrane IDA 19946888
genes like me logo Genes that share ontologies with XAB2: view

Pathways & Interactions 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:0006283 transcription-coupled nucleotide-excision repair TAS --
GO:0006289 nucleotide-excision repair TAS --
GO:0006396 RNA processing IEA --
genes like me logo Genes that share ontologies with XAB2: view

No data available for SIGNOR curated interactions for XAB2 Gene

Drugs & Compounds for XAB2 Gene

No Compound Related Data Available

Transcripts 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

Protein differential expression in normal tissues from HIPED for XAB2 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (19.0) and CD8 Tcells (7.9).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with XAB2: view

Protein tissue co-expression partners for XAB2 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for XAB2 Gene

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 35
  • 99.08 (n)
  • 100 (a)
XAB2 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia XAB2 36
  • 99 (a)
OneToOne
XAB2 35
  • 91.5 (n)
  • 98.95 (a)
dog
(Canis familiaris)
Mammalia XAB2 35
  • 90.72 (n)
  • 98.83 (a)
XAB2 36
  • 99 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Xab2 36
  • 99 (a)
OneToOne
Xab2 16
Xab2 35
  • 89.04 (n)
  • 98.83 (a)
oppossum
(Monodelphis domestica)
Mammalia XAB2 36
  • 90 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 74 (a)
OneToMany
-- 36
  • 86 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Xab2 35
  • 89.55 (n)
  • 98.95 (a)
lizard
(Anolis carolinensis)
Reptilia XAB2 36
  • 78 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.1969 35
tropical clawed frog
(Silurana tropicalis)
Amphibia xab2 35
  • 70.77 (n)
  • 76.46 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4228 35
zebrafish
(Danio rerio)
Actinopterygii xab2 35
  • 74.18 (n)
  • 81.85 (a)
xab2 36
  • 81 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012369 35
  • 70.75 (n)
  • 64.75 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG6197 36
  • 60 (a)
OneToOne
CG6197 35
  • 64.44 (n)
  • 63.63 (a)
worm
(Caenorhabditis elegans)
Secernentea C50F2.3 36
  • 48 (a)
OneToOne
C50F2.3 35
  • 53.65 (n)
  • 49.88 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SYF1 36
  • 22 (a)
OneToOne
SYF1 38
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G28740 35
  • 55.39 (n)
  • 53.62 (a)
rice
(Oryza sativa)
Liliopsida Os.33176 35
Os07g0644300 35
  • 57.35 (n)
  • 52.87 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU08036 35
  • 59.44 (n)
  • 54.16 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes cwf3 35
  • 49.45 (n)
  • 45.6 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.6158 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 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

(1) 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
rs4134822 - 7,627,389(+) GGCGC(A/C/G/T)TCACA reference, missense
rs4134850 - 7,622,772(-) CTTGC(A/G)GCTGC reference, missense
rs4134865 - 7,620,437(-) CCGGC(A/G/T)CGTTC reference, missense
rs794078 -- 7,620,957(+) GCCCT(A/G)GTGGC reference, synonymous-codon
rs794079 -- 7,621,876(+) TAGGA(C/T)TCTGT 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

Variation tolerance for XAB2 Gene

Residual Variation Intolerance Score: 4.24% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.38; 42.15% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for XAB2 Gene

HapMap Linkage Disequilibrium report
XAB2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for XAB2 Gene

Disorders for XAB2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for XAB2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
cockayne syndrome
  • cockayne's syndrome
- elite association - COSMIC cancer census association via MalaCards
Search XAB2 in MalaCards View complete list of genes associated with diseases

Relevant External Links for XAB2

Genetic Association Database (GAD)
XAB2
Human Genome Epidemiology (HuGE) Navigator
XAB2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
XAB2
genes like me logo Genes that share disorders with XAB2: view

No data available for UniProtKB/Swiss-Prot and Genatlas 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 67
  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 23
  3. 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
  4. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. (PMID: 25921289) Emdal K.B. … Olsen J.V. (Sci Signal 2015) 3
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3

Products for XAB2 Gene

Sources for XAB2 Gene

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