Xab2 (XPA binding protein 2) - Rat Genome Database

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Gene: Xab2 (XPA binding protein 2) Rattus norvegicus
Analyze
Symbol: Xab2
Name: XPA binding protein 2
RGD ID: 621217
Description: Involved in cerebral cortex development. Predicted to be located in nucleoplasm. Predicted to be part of Prp19 complex; U2-type catalytic step 2 spliceosome; and post-mRNA release spliceosomal complex. Orthologous to human XAB2 (XPA binding protein 2); PARTICIPATES IN nucleotide excision repair pathway; spliceosome pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: adapter protein ATH-55; Ath-55; Ath55; pre-mRNA-splicing factor SYF1; XPA-binding protein 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2121,667,672 - 1,679,702 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl121,667,672 - 1,679,692 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx122,334,202 - 2,346,238 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0122,957,774 - 2,969,810 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0121,728,678 - 1,740,787 (-)NCBIRnor_WKY
Rnor_6.0122,158,391 - 2,170,397 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl122,158,389 - 2,170,504 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0124,320,723 - 4,332,729 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4122,533,687 - 2,545,690 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1122,533,691 - 2,545,690 (+)NCBI
Celera123,523,414 - 3,535,417 (-)NCBICelera
Cytogenetic Map12p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. A novel rat orthologue and homologue for the Drosophila crooked neck gene in neural stem cells and their immediate descendants. Amada N, etal., J Biochem (Tokyo) 2003 May;133(5):615-23.
2. Splicing and beyond: the many faces of the Prp19 complex. Chanarat S and Strasser K, Biochim Biophys Acta. 2013 Oct;1833(10):2126-34. doi: 10.1016/j.bbamcr.2013.05.023. Epub 2013 Jun 3.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Nucleotide excision repair: new tricks with old bricks. Kamileri I, etal., Trends Genet. 2012 Nov;28(11):566-73. doi: 10.1016/j.tig.2012.06.004. Epub 2012 Jul 22.
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. XAB2, a novel tetratricopeptide repeat protein involved in transcription-coupled DNA repair and transcription. Nakatsu Y, etal., J Biol Chem. 2000 Nov 10;275(45):34931-7.
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
10. GOA pipeline RGD automated data pipeline
11. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
13. Comprehensive gene review and curation RGD comprehensive gene curation
14. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:11991638   PMID:15489334   PMID:15725628   PMID:19946888   PMID:28076346  


Genomics

Comparative Map Data
Xab2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2121,667,672 - 1,679,702 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl121,667,672 - 1,679,692 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx122,334,202 - 2,346,238 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0122,957,774 - 2,969,810 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0121,728,678 - 1,740,787 (-)NCBIRnor_WKY
Rnor_6.0122,158,391 - 2,170,397 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl122,158,389 - 2,170,504 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0124,320,723 - 4,332,729 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4122,533,687 - 2,545,690 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1122,533,691 - 2,545,690 (+)NCBI
Celera123,523,414 - 3,535,417 (-)NCBICelera
Cytogenetic Map12p12NCBI
XAB2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38197,619,525 - 7,629,545 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl197,619,525 - 7,629,545 (-)EnsemblGRCh38hg38GRCh38
GRCh37197,684,411 - 7,694,431 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36197,590,411 - 7,600,439 (-)NCBINCBI36Build 36hg18NCBI36
Build 34197,590,411 - 7,600,439NCBI
Celera197,555,595 - 7,565,623 (-)NCBICelera
Cytogenetic Map19p13.2NCBI
HuRef197,354,087 - 7,364,107 (-)NCBIHuRef
CHM1_1197,684,162 - 7,694,190 (-)NCBICHM1_1
T2T-CHM13v2.0197,620,408 - 7,630,428 (-)NCBIT2T-CHM13v2.0
Xab2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3983,660,089 - 3,671,311 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl83,658,421 - 3,671,316 (-)EnsemblGRCm39 Ensembl
GRCm3883,610,087 - 3,621,334 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl83,608,421 - 3,621,316 (-)EnsemblGRCm38mm10GRCm38
MGSCv3783,610,090 - 3,621,296 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3683,610,090 - 3,621,296 (-)NCBIMGSCv36mm8
Celera83,840,419 - 3,851,625 (-)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map81.92NCBI
Xab2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555631,630,403 - 1,641,037 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555631,630,403 - 1,638,333 (+)NCBIChiLan1.0ChiLan1.0
XAB2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1197,764,264 - 7,774,305 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl197,764,264 - 7,774,305 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0196,909,281 - 6,919,332 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
XAB2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12052,392,521 - 52,406,071 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2052,392,566 - 52,405,997 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2052,196,600 - 52,210,038 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02052,921,824 - 52,935,267 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2052,921,827 - 52,935,293 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12052,125,624 - 52,139,066 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02052,569,168 - 52,582,655 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02052,800,111 - 52,813,660 (-)NCBIUU_Cfam_GSD_1.0
Xab2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118213,154,895 - 213,163,917 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365884,670,841 - 4,679,965 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365884,670,866 - 4,679,888 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
XAB2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl271,521,081 - 71,530,929 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1271,521,034 - 71,530,468 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2271,902,167 - 71,911,580 (-)NCBISscrofa10.2Sscrofa10.2susScr3
XAB2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.167,105,353 - 7,116,063 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl67,104,785 - 7,116,020 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666081745,501 - 756,119 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Xab2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624828704,300 - 712,251 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624828704,400 - 711,963 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Xab2
56 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:46
Count of miRNA genes:41
Interacting mature miRNAs:42
Transcripts:ENSRNOT00000001309
Prediction methods:Microtar, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300174Bw15Body weight QTL 152.93body mass (VT:0001259)body weight loss (CMO:0001399)1219318387Rat
2312418Kidm41Kidney mass QTL 413.70.0001kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)12119611090Rat
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12122591684Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123297788Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12129333307Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
7243862Mcs30Mammary carcinoma susceptibility QTL 308.62mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)127977298525593Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat

Markers in Region
RH141147  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2121,680,757 - 1,681,621 (+)MAPPERmRatBN7.2
Rnor_6.0122,171,479 - 2,172,342NCBIRnor6.0
Rnor_5.0124,333,811 - 4,334,674UniSTSRnor5.0
RGSC_v3.4122,531,742 - 2,532,605UniSTSRGSC3.4
Celera123,536,499 - 3,537,362UniSTS
Cytogenetic Map12p12UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 32 55 39 19 39 1 3 74 35 41 11 1
Low 11 2 2 2 7 8 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001309   ⟹   ENSRNOP00000001309
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl121,667,676 - 1,679,692 (-)Ensembl
Rnor_6.0 Ensembl122,158,389 - 2,170,504 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000109395   ⟹   ENSRNOP00000078127
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl121,667,672 - 1,676,718 (-)Ensembl
RefSeq Acc Id: NM_139109   ⟹   NP_620809
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2121,667,673 - 1,679,676 (-)NCBI
Rnor_6.0122,158,391 - 2,170,397 (-)NCBI
Rnor_5.0124,320,723 - 4,332,729 (-)NCBI
RGSC_v3.4122,533,687 - 2,545,690 (+)RGD
Celera123,523,414 - 3,535,417 (-)RGD
Sequence:
RefSeq Acc Id: XM_039089058   ⟹   XP_038944986
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2121,667,672 - 1,679,702 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_620809   ⟸   NM_139109
- UniProtKB: Q99PK0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000001309   ⟸   ENSRNOT00000001309
RefSeq Acc Id: XP_038944986   ⟸   XM_039089058
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000078127   ⟸   ENSRNOT00000109395

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q99PK0-F1-model_v2 AlphaFold Q99PK0 1-855 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13698370
Promoter ID:EPDNEW_R8895
Type:multiple initiation site
Name:Xab2_1
Description:XPA binding protein 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0122,170,375 - 2,170,435EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621217 AgrOrtholog
BioCyc Gene G2FUF-20393 BioCyc
Ensembl Genes ENSRNOG00000000988 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001309 ENTREZGENE
  ENSRNOP00000001309.3 UniProtKB/TrEMBL
  ENSRNOP00000078127.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001309 ENTREZGENE
  ENSRNOT00000001309.5 UniProtKB/TrEMBL
  ENSRNOT00000109395.1 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7108549 IMAGE-MGC_LOAD
InterPro HAT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Syf1-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TPR-like_helical UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TPR_repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:245976 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93162 IMAGE-MGC_LOAD
NCBI Gene 245976 ENTREZGENE
PANTHER PTHR11246 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam TPR_8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Xab2 PhenoGen
PROSITE TPR UniProtKB/TrEMBL
SMART HAT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TPR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48452 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5XWU2_RAT UniProtKB/TrEMBL
  A0A8L2PZV6_RAT UniProtKB/TrEMBL
  Q99PK0 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Xab2  XPA binding protein 2  Ath55  adapter protein ATH-55  Symbol and Name updated 1299863 APPROVED
2002-08-07 Ath55  adapter protein ATH-55      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized to nuclear pre-mRNA containing splicing complexes 634609
gene_domains contains 21 tetratricopeptide repeat (TPR) motifs 634609
gene_expression expressed in embryonic brain, expression decreases in the adult 634609