Tapbp (TAP binding protein) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Tapbp (TAP binding protein) Rattus norvegicus
Analyze
Symbol: Tapbp
Name: TAP binding protein
RGD ID: 3819
Description: Predicted to enable TAP binding activity; TAP complex binding activity; and antigen binding activity. Involved in MHC class I protein complex assembly. Part of MHC class I peptide loading complex. Human ortholog(s) of this gene implicated in MHC class I deficiency and severe combined immunodeficiency. Orthologous to human TAPBP (TAP binding protein); PARTICIPATES IN antigen processing and presentation pathway; INTERACTS WITH 1,3,5-trinitro-1,3,5-triazinane; 3,3',4,4',5-pentachlorobiphenyl; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: TAP binding protein (tapasin); Tap-binding protein; tapasin
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
mRatBN7.2204,956,937 - 4,966,191 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl204,956,937 - 4,966,181 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx205,681,446 - 5,689,397 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0205,043,191 - 5,051,142 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0205,523,938 - 5,531,891 (-)NCBIRnor_WKY
Rnor_6.0205,468,056 - 5,476,007 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl205,468,078 - 5,476,193 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0207,526,668 - 7,534,862 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4205,109,807 - 5,117,758 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1205,110,035 - 5,117,974 (-)NCBI
Celera206,542,153 - 6,550,105 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3,5-trinitro-1,3,5-triazinane  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
7,12-dimethyltetraphene  (ISO)
acetamide  (EXP)
acrylamide  (EXP,ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antimycin A  (ISO)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzalkonium chloride  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bilirubin IXalpha  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
butan-1-ol  (ISO)
butanal  (ISO)
C60 fullerene  (EXP)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
CGP 52608  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
deguelin  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
dioxygen  (EXP)
disulfiram  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
epoxiconazole  (ISO)
folic acid  (ISO)
fulvestrant  (ISO)
ivermectin  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lipopolysaccharide  (ISO)
methapyrilene  (ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
obeticholic acid  (ISO)
paracetamol  (EXP)
pentachlorophenol  (ISO)
picoxystrobin  (ISO)
protein kinase inhibitor  (ISO)
resveratrol  (ISO)
selenium atom  (ISO)
sodium arsenite  (ISO)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (EXP)
Triptolide  (EXP)
triptonide  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
zoledronic acid  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Rat tapasin: cDNA cloning and identification as a component of the class I MHC assembly complex. Deverson EV, etal., Genes Immun 2001 Feb;2(1):48-51.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
8. GOA pipeline RGD automated data pipeline
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Molecular architecture of the TAP-associated MHC class I peptide-loading complex. Rufer E, etal., J Immunol. 2007 Nov 1;179(9):5717-27.
12. 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.
13. Differential expression of tapasin and immunoproteasome subunits in adenovirus type 5- versus type 12-transformed cells. Vertegaal AC, etal., J Biol Chem 2003 Jan 3;278(1):139-46.
14. The varicellovirus UL49.5 protein blocks the transporter associated with antigen processing (TAP) by inhibiting essential conformational transitions in the 6+6 transmembrane TAP core complex. Verweij MC, etal., J Immunol. 2008 Oct 1;181(7):4894-907.
15. A subject with a novel type I bare lymphocyte syndrome has tapasin deficiency due to deletion of 4 exons by Alu-mediated recombination. Yabe T, etal., Blood. 2002 Aug 15;100(4):1496-8.
Additional References at PubMed
PMID:9716645   PMID:10981964   PMID:11884415   PMID:12047747   PMID:12582157   PMID:12594855   PMID:21263072   PMID:24586191  


Genomics

Comparative Map Data
Tapbp
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,956,937 - 4,966,191 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl204,956,937 - 4,966,181 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx205,681,446 - 5,689,397 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0205,043,191 - 5,051,142 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0205,523,938 - 5,531,891 (-)NCBIRnor_WKY
Rnor_6.0205,468,056 - 5,476,007 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl205,468,078 - 5,476,193 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0207,526,668 - 7,534,862 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4205,109,807 - 5,117,758 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1205,110,035 - 5,117,974 (-)NCBI
Celera206,542,153 - 6,550,105 (-)NCBICelera
Cytogenetic Map20p12NCBI
TAPBP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38633,299,694 - 33,314,078 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl633,299,694 - 33,314,284 (-)EnsemblGRCh38hg38GRCh38
GRCh37633,267,471 - 33,281,855 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36633,375,449 - 33,389,967 (-)NCBINCBI36Build 36hg18NCBI36
Build 34633,380,022 - 33,389,967NCBI
Celera634,821,829 - 34,836,529 (-)NCBICelera
Cytogenetic Map6p21.32NCBI
HuRef633,009,105 - 33,023,734 (-)NCBIHuRef
CHM1_1633,269,408 - 33,284,098 (-)NCBICHM1_1
T2T-CHM13v2.0633,121,056 - 33,135,440 (-)NCBIT2T-CHM13v2.0
Tapbp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391734,138,452 - 34,148,264 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1734,134,873 - 34,148,266 (+)EnsemblGRCm39 Ensembl
GRCm381733,919,478 - 33,929,290 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1733,915,899 - 33,929,292 (+)EnsemblGRCm38mm10GRCm38
MGSCv371734,056,423 - 34,066,235 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361733,529,932 - 33,539,744 (+)NCBIMGSCv36mm8
Celera1736,672,402 - 36,682,204 (+)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1717.98NCBI
Tapbp
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554371,858,328 - 1,866,233 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554371,860,057 - 1,865,645 (-)NCBIChiLan1.0ChiLan1.0
TAPBP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1633,986,058 - 34,000,190 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl633,986,058 - 34,000,190 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0632,871,768 - 32,886,679 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
TAPBP
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1122,740,276 - 2,751,808 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl122,740,276 - 2,751,808 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha122,821,151 - 2,832,681 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0123,071,694 - 3,083,242 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl123,071,399 - 3,083,239 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1122,738,920 - 2,750,427 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0122,820,202 - 2,831,740 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0122,895,118 - 2,906,650 (-)NCBIUU_Cfam_GSD_1.0
Tapbp
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494638,393,629 - 38,405,741 (-)NCBIHiC_Itri_2
SpeTri2.0NW_00493647625,554,186 - 25,566,634 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TAPBP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl729,663,495 - 29,673,634 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1729,663,491 - 29,673,453 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2734,167,262 - 34,176,655 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TAPBP
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11738,762,934 - 38,776,247 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1738,763,206 - 38,773,768 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604433,134,294 - 33,149,129 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tapbp
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475423,509,436 - 23,520,135 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475423,513,060 - 23,521,169 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Position Markers
Zfp297  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,967,225 - 4,967,679 (+)MAPPERmRatBN7.2
Rnor_6.0205,477,240 - 5,477,693NCBIRnor6.0
Rnor_5.0207,535,852 - 7,536,305UniSTSRnor5.0
RGSC_v3.4205,118,991 - 5,119,444UniSTSRGSC3.4
Celera206,551,338 - 6,551,791UniSTS
Cytogenetic Map20p12UniSTS
RH130697  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,966,524 - 4,966,741 (+)MAPPERmRatBN7.2
Rnor_6.0205,476,539 - 5,476,755NCBIRnor6.0
Rnor_5.0207,535,151 - 7,535,367UniSTSRnor5.0
RGSC_v3.4205,118,290 - 5,118,506UniSTSRGSC3.4
Celera206,550,637 - 6,550,853UniSTS
RH 3.4 Map2054.2UniSTS
Cytogenetic Map20p12UniSTS
BE106728  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,958,482 - 4,958,639 (+)MAPPERmRatBN7.2
Rnor_6.0205,468,498 - 5,468,654NCBIRnor6.0
Rnor_5.0207,527,110 - 7,527,266UniSTSRnor5.0
RGSC_v3.4205,110,249 - 5,110,405UniSTSRGSC3.4
Celera206,542,595 - 6,542,751UniSTS
RH 3.4 Map2055.8UniSTS
Cytogenetic Map20p12UniSTS
BF390203  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,964,519 - 4,964,684 (+)MAPPERmRatBN7.2
Rnor_6.0205,474,534 - 5,474,698NCBIRnor6.0
Rnor_5.0207,533,146 - 7,533,310UniSTSRnor5.0
RGSC_v3.4205,116,285 - 5,116,449UniSTSRGSC3.4
Celera206,548,632 - 6,548,796UniSTS
RH 3.4 Map2056.24UniSTS
Cytogenetic Map20p12UniSTS
UniSTS:237624  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,966,369 - 4,966,552 (+)MAPPERmRatBN7.2
Rnor_6.0205,476,384 - 5,476,566NCBIRnor6.0
Rnor_5.0207,534,996 - 7,535,178UniSTSRnor5.0
RGSC_v3.4205,118,135 - 5,118,317UniSTSRGSC3.4
Celera206,550,482 - 6,550,664UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036216499243559Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2046066076691706Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat
7175096Tcs1T cell selection QTL 1T cell selectionexpression2047270785024580Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:109
Count of miRNA genes:90
Interacting mature miRNAs:96
Transcripts:ENSRNOT00000044975
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.


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 35 57 41 19 41 3 5 12 29 34 11 3
Low 8 5 6 62 6 7 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000044975   ⟹   ENSRNOP00000045630
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,959,480 - 4,966,181 (-)Ensembl
Rnor_6.0 Ensembl205,468,078 - 5,476,193 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092362   ⟹   ENSRNOP00000075928
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,469,582 - 5,469,966 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099978   ⟹   ENSRNOP00000078929
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,956,937 - 4,966,181 (-)Ensembl
RefSeq Acc Id: NM_033098   ⟹   NP_149089
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,958,041 - 4,965,993 (-)NCBI
Rnor_6.0205,468,056 - 5,476,007 (-)NCBI
Rnor_5.0207,526,668 - 7,534,862 (-)NCBI
RGSC_v3.4205,109,807 - 5,117,758 (-)RGD
Celera206,542,153 - 6,550,105 (-)RGD
Sequence:
RefSeq Acc Id: XM_039098437   ⟹   XP_038954365
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,956,937 - 4,966,191 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_149089   ⟸   NM_033098
- Peptide Label: precursor
- UniProtKB: Q99JC6 (UniProtKB/TrEMBL),   F1MAR8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075928   ⟸   ENSRNOT00000092362
RefSeq Acc Id: ENSRNOP00000045630   ⟸   ENSRNOT00000044975
RefSeq Acc Id: XP_038954365   ⟸   XM_039098437
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000078929   ⟸   ENSRNOT00000099978
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q99JC6-F1-model_v2 AlphaFold Q99JC6 1-464 view protein structure

Transcriptome

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

Promoters
RGD ID:13701414
Promoter ID:EPDNEW_R11937
Type:multiple initiation site
Name:Tapbp_1
Description:TAP binding protein
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R11938  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0205,476,011 - 5,476,071EPDNEW
RGD ID:13701415
Promoter ID:EPDNEW_R11938
Type:initiation region
Name:Tapbp_2
Description:TAP binding protein
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R11937  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0205,476,216 - 5,476,276EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 5475701 5475702 C A snv MNS/Gib (RGD), WAG/RijCrl (2020), FHL/EurMcwi (MCW), SBN/Ygl (MCW), MWF/Hsd (2019), FHL/EurMcwi (RGD), MHS/Gib (RGD), SBN/Ygl (RGD), WAG/Rij (RGD), MR/N (MCW)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 7534313 7534314 C A snv FHL/EurMcwi (MCW), ZF (KyushuU), MHS/Gib (KNAW), MR/N (KNAW), WAG/Rij (KNAW), BBDP/WorN (KNAW), FHL/EurMcwi (KNAW), MNS/Gib (KNAW), SBN/Ygl (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL), BUF/MNa (KyushuU), HTX/Kyo (KyushuU), RCS/Kyo (KyushuU), LEC/Tj (KyushuU), KFRS3B/Kyo (KyushuU), SBN/Ygl (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 5117452 5117453 C A snv FHL/EurMcwi (MCW), MR/N (KNAW), BBDP/WorN (ICL), WAG/Rij (ICL), MHS/Gib (ICL), MNS/Gib (ICL), SBN/Ygl (ICL), FHL/EurMcwi (ICL)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 4965687 4965688 C A snv WAG/RijCrl (2020), MWF/Hsd (2019)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3819 AgrOrtholog
BioCyc Gene G2FUF-4515 BioCyc
Ensembl Genes ENSRNOG00000029500 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000045630.4 UniProtKB/TrEMBL
  ENSRNOP00000078929 ENTREZGENE
  ENSRNOP00000078929.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044975.5 UniProtKB/TrEMBL
  ENSRNOT00000099978 ENTREZGENE
  ENSRNOT00000099978.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:5599850 IMAGE-MGC_LOAD
InterPro Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig/MHC_CS UniProtKB/TrEMBL
  Ig_C1-set UniProtKB/TrEMBL
  Tapasin UniProtKB/TrEMBL
KEGG Report rno:25217 UniProtKB/TrEMBL
MGC_CLONE MGC:72337 IMAGE-MGC_LOAD
NCBI Gene 25217 ENTREZGENE
Pfam C1-set UniProtKB/TrEMBL
PhenoGen Tapbp PhenoGen
PRINTS TAPASIN UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt A0A023IM54_RAT UniProtKB/TrEMBL
  A0A8I5ZLY7_RAT UniProtKB/TrEMBL
  A0A8J8Y6W0_RAT UniProtKB/TrEMBL
  F1MAR8 ENTREZGENE
  Q99JC6 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary F1MAR8 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-08-19 Tapbp  TAP binding protein  Tapbp  TAP binding protein (tapasin)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-02-02 Tapbp  TAP binding protein (tapasin)  Tapbp  TAP binding protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Tapbp  TAP binding protein  Tapasin  Tap-binding protein  Symbol and Name updated 629477 APPROVED
2002-06-10 Tapasin  Tap-binding protein      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_mapping found in the major histocompatibility RT1 complex 1300431