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XAB2 Gene

protein-coding   GIFtS: 60

GC19M007590
XPA binding protein 2
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
DKFZp762C1015 2
HCNP 1, 2, 3
HCRN 1, 2
KIAA1177 3
NTC90 1, 2
SYF1 1, 2, 3
Descriptions
Protein HCNP 3
SYF1 homolog, RNA splicing factor 2
XPA binding protein 2 2
XPA-binding protein 2 3
crn-related protein kim1 2
External Ids
HGNC: 140891
Entrez Gene: 569492
UniProtKB: Q9HCS73
Ensembl: ENSG000000769247
Search outside databases for aliases for XAB2 gene

Previous GC identifer: GC00U913006

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: SYF1_HUMAN, Q9HCS7
Function: Involved in transcription-coupled repair (TCR), transcription and pre-mRNA splicing

Gene Wiki entry for XAB2

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the XAB2 gene  

Entrez Gene cytogenetic band: 19p13.2   Ensembl cytogenetic band:  19p13.2   HGNC cytogenetic band: 19p13.3

XAB2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M007590:     (about GC identifiers)

Start:
7,590,411 bp from pter
End:
7,600,439 bp from pter
Size:
10,029 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000019.8  NT_077812.2  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: SYF1_HUMAN, Q9HCS7 (See protein sequence)
Recommended Name: Pre-mRNA-splicing factor SYF1  
Size: 855 amino acids; 100010 Da
Subunit: Associates with RNA polymerase II, the TCR-specific proteins CKN1/CSA and ERCC6/CSB, and
XPA. Identified in the spliceosome C complex, at least composed of AQR, ASCC3L1, C19orf29, CDC40,
CDC5L, CRNKL1, DDX23, DDX41, DDX48, DDX5, DGCR14, DHX35, DHX38, DHX8, EFTUD2, FRG1, GPATC1,
HNRPA1, HNRPA2B1, HNRPA3, HNRPC, HNRPF, HNRPH1, HNRPK, HNRPM, HNRPR, HNRPU, KIAA1160, KIAA1604,
LSM2, LSM3, MAGOH, MORG1, PABPC1, PLRG1, PNN, PPIE, PPIL1, PPIL3, PPWD1, PRPF19, PRPF4B, PRPF6,
PRPF8, RALY, RBM22, RBM8A, RBMX, SART1, SF3A1, SF3A2, SF3A3, SF3B1, SF3B2, SF3B3, SFRS1, SKIV2L2,
SNRPA1, SNRPB, SNRPB2, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, SNW1, SRRM1, SRRM2, SYF2,
SYNCRIP, TFIP11, THOC4, U2AF1, WDR57, XAB2 and ZCCHC8
Subcellular location: Nucleus (By similarity). Note=Detected in the splicing complex carrying
pre-mRNA (By similarity)
Sequence caution: Sequence=AAF86951.1; Type=Frameshift; Positions=314, 411, 426, 429, 468;
Sequence=BAB84861.1; Type=Miscellaneous discrepancy; Note=Alternative splicing. Incomplete
sequence. Incomplete sequence;
Secondary accessions: Q8TET6 Q96HB0 Q96IW0 Q9NRG6 Q9ULP3

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_064581.2  

    ENSEMBL proteins: 
    ENSP00000351137 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Browse Human Recombinant Proteins at Sigma-Aldrich  
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (XAB2)
    Human Recombinant Proteins from Abnova (XAB2)
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    4 Gene Ontology (GO) cellular component terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622 intracellular IEA--
    GO:0005634 nucleus IC10944529
    GO:0005654 nucleoplasm EXP11313499
    GO:0005681 spliceosome IEA--
    About this table

    Antibodies for XAB2: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for XAB2
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (XAB2), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (XAB2)
    Novus Biologicals Antibodies for XAB2

    Assays for XAB2: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    2 InterPro domains/families:
     IPR011990 TPR-like_helical
     IPR003107 HAT


       GeneDecks  XAB2 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q9HCS7

    ProtoNet protein and cluster: Q9HCS7

    1 Blocks protein family: IPB003107 RNA-processing protein

    UniProtKB/Swiss-Prot: SYF1_HUMAN, Q9HCS7
    Similarity: Belongs to the crooked-neck family
    Similarity: Contains 14 HAT repeats

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (XAB2)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (XAB2)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_020196

                  Applied Biosystems Silencer® siRNAs for XAB2

                  Sigma-Aldrich siRNA for XAB2  
                         Sigma-Aldrich shRNA Panels and shRNA for XAB2  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for XAB2
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_020196
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_020196
                                     untagged cDNA clone in CMV expression vector: NM_020196 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_020196

    UniProtKB/Swiss-Prot: SYF1_HUMAN, Q9HCS7
    Function: Involved in transcription-coupled repair (TCR), transcription and pre-mRNA splicing

    2 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Xab2):

    embryogenesislethality-prenatal/perinatal

    1 Gene Ontology (GO) molecular function term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515 protein binding IPI10944529
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section


     Gene Network CentralTM Interacting Genes and Proteins Network for  XAB2 


    5/44 Interacting proteins for XAB2 (Q9HCS71, 2 ENSP000003511373) via UniProtKB, MINT, and/or STRING (see all 44 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ERCC8Q132161, ENSP000002650383EBI-295232, EBI-295260 STRING (score=.99)
    POLR2AP249281, ENSP000003149493EBI-295232, EBI-295301 STRING (score=.971)
    XPAP230251, ENSP000003642703EBI-295232, EBI-295222 STRING (score=.927)
    GLIS2Q9BZE02MINT-4651467
    ERCC6ENSP000003480893STRING (score=.99)
    About this table

    5/7 Gene Ontology (GO) biological process terms (links to tree view) (see all 7 ):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001824 blastocyst development IEA--
    GO:0006281 DNA repair IEA--
    GO:0006283 transcription-coupled nucleotide-excision repair IDA10944529
    GO:0006350 transcription IDA10944529
    GO:0006397 mRNA processing IEA--
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for XAB2

    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (XAB2)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (XAB2)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_020196

                  Sigma-Aldrich siRNA for XAB2  
                         Sigma-Aldrich shRNA Panels and shRNA for XAB2  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_020196  

    REFSEQ mRNAs for XAB2 gene: 

    NM_020196.2   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_020196  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_020196
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_020196
                                     untagged cDNA clone in CMV expression vector: NM_020196 

    Additional cDNA sequence: 

    AB026111.1 AB033003.1 AF226051.1 AF258567.1 AF272147.1 AK025858.1 AK074035.1 BC007208.1 
    BC008778.1 CR591175.1 CR603946.1 CR615253.1 CR615981.1 CR749864.1 

    7 DOTS entries:

    DT.445941  DT.91755990  DT.97759948  DT.100833965  DT.95144979  DT.95133035  DT.95144980 

    24/272 AceView cDNA sequences (see all 272 ):

    CA488373 BQ050225 CR615253 CR603946 BM917523 CR615981 AA722714 BE514810 
    BM836134 BU845857 CR749864 F35523 AA351089 AB033003 AL525436 BU179797 
    AL534944 BI772072 BQ927835 BQ643137 BQ053451 BE383420 F02416 BC007208 

    highest scoring ESTs for XAB2:

    AA160389 AA811391 AB026111 AF226051 AF258567 AF272147 AL514374 AL518679 AL519886 AL525436 

    Unigene Cluster for XAB2:

    XPA binding protein 2
    Hs.9822  [show with all ESTs]
    Unigene Representative Sequence: AK074035


    GeneLoc Exon Structure

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

    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:                                                                                                                                                

    About this scheme

    ECgene alternative splicing isoforms for XAB2

    1 Ensembl transcript including schematic representation:
    ENST00000358368  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    XAB2 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for XAB2

    1 / 2 / 3

    3 probe-sets matching XAB2 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    47620_at2, 3 U95-B 1 1.00 1.00 1.00 1.00 AA811391 0.80 1.00 0.91 1

    218110_at2, 3 U133-A 1 1.00 1.00 -- -- NM_020196 0.60 1.00 0.82 1

    218110_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    GeneDecks  XAB2 for binary patterns associated with the probe-sets selected above  
    About GeneDecksing
    About this table    
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: AAGCTGCTGG

    SOURCE GeneReport for Unigene cluster: Hs.9822
    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for XAB2 gene from 5/17 species (see all 17 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    XAB21   -- XPA binding protein 2 90.69(n)
    98.83(a)
    484995  XM_849080.1  XP_854173.1 
    cow
    (Bos taurus)
    XAB21   -- XPA binding protein 2 91.5(n)
    98.95(a)
    528991  NM_001075919.1  NP_001069387.1 
    rat
    (Rattus norvegicus)
    Xab21   -- XPA binding protein 2 89.55(n)
    98.95(a)
    245976  NM_139109.1  NP_620809.1 
    mouse
    (Mus musculus)
    Xab21, 5 8 (1.00 cM)5
    XPA binding protein 21, 5 89.04(n)1
    98.83(a)1
    674391  NM_026156.21  NP_080432.11 
     AI4147065  AI8516505  (see all 20)
    zebrafish
    (Danio rerio)
    xab22   -- XPA binding protein 2 76.02(n) 387600  BC054579.1 
    About this table        Species with no ortholog for XAB2

    ENSEMBL Gene Tree for XAB2
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for XAB2 gene
    PRPF62  CRNKL12  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/94 NCBI SNPs in XAB2 are shown (see all 94 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 89)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 19 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs41348731,2
    C,F,H7590128(-) CCTCTC/AAGAGC 1 -- ng518Minor allele frequency- A:0.04NS EU EA WA NA 726
    rs41348721,2
    C,F,H7590171(-) AGGGCA/GATCCA 1 -- ng5114Minor allele frequency- G:0.04NS EU EA WA NA 1398
    --
    rs41348711,2
    C,F7590238(-) CCTCCG/ACTGCC 1 -- ng514Minor allele frequency- A:0.01NS NA 318
    --
    rs41348701,2
    F7590451(-) CCCCCATCC    
       CCC
    /-
    CTCCC
    1 -- ut311Minor allele frequency- -:0.15NS 178
    rs41348651,2
    H7591323(-) CCGGCG/ACGTTC 1 T/A mis1 ese35Minor allele frequency- A:0.00NS EU EA WA 590
    rs41348741,2
    H7589959(-) CAGGCG/ACCAGA 1 -- ng515Minor allele frequency- A:0.00NS EU EA WA 544
    rs7940781,2
    C,F,H7591843(+) GCCCTA/GGTGGC 1 T/T syn1 ese320Minor allele frequency- N:0.00NS MN EU EA WA NA 2046
    rs41348661,2
    C,F,H7591183(-) AAGGTC/TTCGGG 1 V/V syn1 ese36Minor allele frequency- T:0.01NS EU EA WA NA 664
    rs41348691,2
    C,F,H7590502(-) CCAGCC/TGCAGT 1 A/A syn1 ese314Minor allele frequency- T:0.06NS EU EA WA NA 1394
    --
    rs41348391,2
    C,F7596892(-) AATCCG/AGACAA 1 P/P syn1 ese310Minor allele frequency- A:0.02NS NA 980
    About this table

    HapMap Linkage Disequilibrium images for XAB2 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 610850

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/15 PubMed articles for XAB2 gene (see all 15 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)
    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
    About This Section

    Entrez Gene: 56949 HGNC: 14089 AceView: XAB2 Ensembl:ENSG00000076924 euGenes: HUgn56949
    ECgene: XAB2 H-InvDB: XAB2
    (According to HUGE)
    About This Section

    HUGE: KIAA1177
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

    NameDescription
    ATLAS Chromosomes in Cancer entry for XAB2 Genetics and Cytogenetics in Oncology and Haematology
    NIEHS-SNPshttp://egp.gs.washington.edu/data/hcnp/
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for XAB2:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for XAB2 Antibodies for XAB2
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
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