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Aliases & Descriptions for XAB2
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc
, and/or 7Ensembl,
8miRBase) About This Section
|
| 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 |
|
| | Search outside databases for aliases for XAB2 genePrevious GC identifer: GC00U913006 |
Summaries for XAB2(According to Entrez Gene,
Wikipedia's
Gene Wiki,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
| UniProtKB/Swiss-Prot: SYF1_HUMAN, Q9HCS7Function: Involved in transcription-coupled repair (TCR), transcription and pre-mRNA splicingGene Wiki entry for XAB2 |
Genomic Location 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: 19p13.3XAB2 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
| Proteins for XAB2
(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)
About This Section
| 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 Q9ULP3Post-translational modifications:
View phosphorylation sites using PhosphoSite2
REFSEQ proteins: NP_064581.2
ENSEMBL proteins: ENSP00000351137
Human Recombinant Proteins Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 
4 Gene Ontology (GO) cellular component terms (links to tree view): About this table
Antibodies for XAB2: Assays for XAB2: | Protein
Domains/ Families for XAB2(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
| - 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, Q9HCS7Similarity: Belongs to the crooked-neck familySimilarity: Contains 14 HAT repeats | Gene Function for XAB2
(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
|               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 
              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, Q9HCS7Function: Involved in transcription-coupled repair (TCR), transcription and pre-mRNA splicing2 MGI mutant phenotypes (inferred from 2 alleles ) (MGI details for Xab2):
1 Gene Ontology (GO) molecular function term (links to tree view): About this table | Pathways & Interactions for XAB2
(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
)About this table
5/7 Gene Ontology (GO) biological process terms (links to tree view) (see all 7
): About this table
|
Drugs & Compounds for XAB2(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 Tocris compounds for XAB2
|
Transcripts 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
|               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
|
Expression for XAB2
(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 Data from
(Publications) and GNF BioGPS About these images About these images
CGAP SAGE TAG: AAGCTGCTGG
SOURCE GeneReport for Unigene cluster: Hs.9822
|
Orthologs for XAB2
(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
)
About this table Species with no ortholog for XAB2
ENSEMBL Gene Tree for XAB2 | Paralogs for XAB2(Paralogs according to 1HomoloGene and 2Ensembl, Pseudogenes according to 3Pseudogene.org) About This Section
| Paralogs for XAB2 gene
- PRPF62 CRNKL12
|
SNPs/Variants for XAB2(According to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE, and
UniProtKB,
Linkage Disequilibrium by HapMap,
Genotyping Reagents from
Applied Biosystems)
About This Section
|
HapMap Linkage Disequilibrium images for XAB2 (up to first 250kb)
|
Disorders & Mutations for XAB2
(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
|
Medical News for XAB2(Possibly Related Articles in
Doctor's Guide)
About This Section
| -- |
Publications for XAB2 (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
):- XAB2, a novel tetratricopeptide repeat protein, involved in transcription-coupled DNA repair and transcription. (PubMed id 10944529)1, 2, 3, 4 Nakatsu Y.... Tanaka K. (2000)
- The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)3, 4 Gerhard D.S....Malek J. (2004)
- Large-scale cDNA transfection screening for genes related to cancer development and progression. (PubMed id 15498874)3, 4 Wan D....Gu J. (2004)
- Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. (PubMed id 11991638)3, 4 Jurica M.S.... Moore M.J. (2002)
- Characterization of cDNA clones selected by the GeneMark analysis from size-fractionated cDNA libraries from human brain. (PubMed id 10574461)3, 4 Hirosawa M....Ohara O. (1999)
- Isolation of XAB2 complex involved in pre-mRNA splicing, transcription, and transcription-coupled repair. (PubMed id 17981804)1, 3 Kuraoka I....Tanaka K. (2008)
- A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)4 Dephoure N.... Gygi S.P. (2008)
- Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)3 Rual J.F....Vidal M. (2005)
- Functional proteomics mapping of a human signaling pathway. (PubMed id 15231748)3 Colland F....Gauthier J.M. (2004)
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)3 Ota T....Sugano S. (2004)
|
Search for XAB2
(in PubMed,
OMIM, and NCBI Bookshelf) About This Section
|
|
Genome Databases showing XAB2
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
and/or
H-InvDB)
About This Section
|
| Other Databases showing XAB2
(According to HUGE)
About This Section
| |
Specialized Databases showing XAB2(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
|
| About This Section
| --
| Services for XAB2(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:

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Incremental update: 13 Oct 2009
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