Arid1a (AT-rich interaction domain 1A) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Arid1a (AT-rich interaction domain 1A) Rattus norvegicus
Analyze
Symbol: Arid1a
Name: AT-rich interaction domain 1A
RGD ID: 1310500
Description: Predicted to enable ATP-dependent chromatin remodeler activity; DNA binding activity; and nuclear receptor binding activity. Predicted to contribute to nucleosome binding activity. Predicted to be involved in intracellular steroid hormone receptor signaling pathway; nucleosome disassembly; and regulation of DNA-templated transcription. Predicted to act upstream of or within several processes, including circulatory system development; embryonic morphogenesis; and toxin transport. Predicted to be located in chromatin. Predicted to be part of SWI/SNF complex; nBAF complex; and npBAF complex. Predicted to be active in nucleoplasm. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 2; breast cancer; carcinoma (multiple); gastrointestinal system cancer (multiple); and neuroblastoma. Orthologous to human ARID1A (AT-rich interaction domain 1A); PARTICIPATES IN altered SWI/SNF family mediated chromatin remodeling pathway; pancreatic cancer pathway; SWI/SNF family mediated chromatin remodeling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: AT rich interactive domain 1A (SWI-like); AT rich interactive domain 1A (Swi1 like); AT-rich interactive domain-containing protein 1A; LOC297867
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
mRatBN7.25145,908,181 - 145,981,609 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5145,908,181 - 145,985,564 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5148,610,576 - 148,683,764 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.05150,380,181 - 150,453,373 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.05150,366,738 - 150,439,933 (-)NCBIRnor_WKY
Rnor_6.05151,904,687 - 151,977,973 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5151,904,684 - 151,977,636 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05155,592,617 - 155,665,889 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45151,355,617 - 151,398,647 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15151,335,330 - 151,408,688 (+)NCBI
Celera5144,329,185 - 144,372,216 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Acute Hepatitis  (ISO)
adenocarcinoma  (ISO)
adenoid cystic carcinoma  (ISO)
breast cancer  (ISO)
Breast Neoplasms  (ISO)
Burkitt lymphoma  (ISO)
cerebellar hypoplasia  (ISO)
cholangiocarcinoma  (ISO)
Coffin-Siris syndrome  (ISO)
Coffin-Siris syndrome 1  (ISO)
Coffin-Siris syndrome 2  (ISO)
colon adenocarcinoma  (ISO)
colon cancer  (ISO)
colorectal cancer  (ISO)
colorectal carcinoma  (ISO)
Colorectal Neoplasms  (ISO)
embryonal rhabdomyosarcoma  (ISO)
endometrial adenocarcinoma  (ISO)
endometrial cancer  (ISO)
Endometrial Neoplasms  (ISO)
epilepsy  (ISO)
esophagus adenocarcinoma  (ISO)
Experimental Liver Neoplasms  (ISO)
gastric adenocarcinoma  (ISO)
genetic disease  (ISO)
hepatoblastoma  (ISO)
hepatocellular carcinoma  (ISO)
Hydrops Fetalis  (ISO)
intellectual disability  (ISO)
intrahepatic cholangiocarcinoma  (ISO)
Klatskin's tumor  (ISO)
lung cancer  (ISO)
lung non-small cell carcinoma  (ISO)
lung squamous cell carcinoma  (ISO)
Marfanoid Mental Retardation Syndrome, Autosomal  (ISO)
medulloblastoma  (ISO)
microcephaly  (ISO)
Microsatellite Instability  (ISO)
nasopharynx carcinoma  (ISO)
Neoplasm Metastasis  (ISO)
nephroblastoma  (ISO)
neuroblastoma  (ISO)
Neurodevelopmental Disorders  (ISO)
non-functioning pancreatic endocrine tumor  (ISO)
ovarian clear cell carcinoma  (ISO)
ovary serous adenocarcinoma  (ISO)
pancreatic cancer  (ISO)
periventricular leukomalacia  (ISO)
primary cutaneous T-cell non-Hodgkin lymphoma  (ISO)
Prostatic Neoplasms  (ISO)
septooptic dysplasia  (ISO)
Sezary's disease  (ISO)
small intestine carcinoma  (ISO)
stomach cancer  (ISO)
stomach carcinoma  (ISO)
Stomach Neoplasms  (ISO)
T-Cell Lymphoma  (ISO)
transitional cell carcinoma  (ISO)
urinary bladder cancer  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,4,6-tribromophenol  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
4,4'-sulfonyldiphenol  (ISO)
aflatoxin B1  (ISO)
aristolochic acid A  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
buta-1,3-diene  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
choline  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
coumarin  (ISO)
crocidolite asbestos  (ISO)
decabromodiphenyl ether  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dicrotophos  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
furan  (EXP)
gentamycin  (EXP)
hexadecanoic acid  (ISO)
indometacin  (ISO)
L-methionine  (ISO)
Lasiocarpine  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
methamphetamine  (ISO)
methidathion  (ISO)
methotrexate  (ISO)
methylmercury chloride  (ISO)
monocrotaline  (ISO)
nefazodone  (EXP)
nicotine  (ISO)
paracetamol  (EXP,ISO)
PCB138  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
profenofos  (EXP)
promegestone  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
thioacetamide  (EXP)
trichostatin A  (ISO)
Triptolide  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zinc atom  (ISO)
zinc(0)  (ISO)

References

References - curated
# Reference Title Reference Citation
1. High Beclin-1 and ARID1A expression corelates with poor survival and high recurrence in intrahepatic cholangiocarcinoma: a histopathological retrospective study. Bi C, etal., BMC Cancer. 2019 Mar 8;19(1):213. doi: 10.1186/s12885-019-5429-3.
2. Hepatocyte-Specific Arid1a Deficiency Initiates Mouse Steatohepatitis and Hepatocellular Carcinoma. Fang JZ, etal., PLoS One. 2015 Nov 16;10(11):e0143042. doi: 10.1371/journal.pone.0143042. eCollection 2015.
3. Comprehensive analysis of genomic alterations of Chinese hilar cholangiocarcinoma patients. Feng F, etal., Int J Clin Oncol. 2021 Apr;26(4):717-727. doi: 10.1007/s10147-020-01846-z. Epub 2021 Jan 2.
4. 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.
5. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
6. ARID1A, a factor that promotes formation of SWI/SNF-mediated chromatin remodeling, is a tumor suppressor in gynecologic cancers. Guan B, etal., Cancer Res. 2011 Nov 1;71(21):6718-27. doi: 10.1158/0008-5472.CAN-11-1562. Epub 2011 Sep 7.
7. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Hargreaves DC and Crabtree GR, Cell Res. 2011 Mar;21(3):396-420. doi: 10.1038/cr.2011.32. Epub 2011 Mar 1.
8. Decreased expression of ARID1A associates with poor prognosis and promotes metastases of hepatocellular carcinoma. He F, etal., J Exp Clin Cancer Res. 2015 May 15;34:47. doi: 10.1186/s13046-015-0164-3.
9. Arid1a regulates response to anti-angiogenic therapy in advanced hepatocellular carcinoma. Hu C, etal., J Hepatol. 2018 Mar;68(3):465-475. doi: 10.1016/j.jhep.2017.10.028. Epub 2017 Nov 4.
10. ARID1A expression in gastric adenocarcinoma: clinicopathological significance and correlation with DNA mismatch repair status. Inada R, etal., World J Gastroenterol. 2015 Feb 21;21(7):2159-68. doi: 10.3748/wjg.v21.i7.2159.
11. Associations Between Loss of ARID1A Expression and Clinicopathologic and Genetic Variables in T1 Early Colorectal Cancer. Kishida Y, etal., Am J Clin Pathol. 2019 Sep 9;152(4):463-470. doi: 10.1093/ajcp/aqz062.
12. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
13. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
14. AT-rich Interaction Domain 1A Gene Variations: Genetic Associations and Susceptibility to Gastric Cancer Risk. Qadir J, etal., Pathol Oncol Res. 2020 Oct;26(4):2237-2246. doi: 10.1007/s12253-020-00815-1. Epub 2020 May 6.
15. GOA pipeline RGD automated data pipeline
16. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
18. Comprehensive gene review and curation RGD comprehensive gene curation
19. Heterogeneity of ARID1A expression in gastric cancer may affect patient survival and therapeutic efficacy. Saito M, etal., Hum Pathol. 2020 Jul;101:80-81. doi: 10.1016/j.humpath.2020.04.009. Epub 2020 May 7.
20. Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma. Sausen M, etal., Nat Genet. 2013 Jan;45(1):12-7. doi: 10.1038/ng.2493. Epub 2012 Dec 2.
21. Loss of the SWI/SNF-ATPase subunit members SMARCF1 (ARID1A), SMARCA2 (BRM), SMARCA4 (BRG1) and SMARCB1 (INI1) in oesophageal adenocarcinoma. Schallenberg S, etal., BMC Cancer. 2020 Jan 6;20(1):12. doi: 10.1186/s12885-019-6425-3.
22. The spectrum of SWI/SNF mutations, ubiquitous in human cancers. Shain AH and Pollack JR, PLoS One. 2013;8(1):e55119. doi: 10.1371/journal.pone.0055119. Epub 2013 Jan 23.
23. ARID1A Deficiency Impairs the DNA Damage Checkpoint and Sensitizes Cells to PARP Inhibitors. Shen J, etal., Cancer Discov. 2015 Jul;5(7):752-67. doi: 10.1158/2159-8290.CD-14-0849. Epub 2015 Jun 11.
24. Subunits of ARID1 serve as novel biomarkers for the sensitivity to immune checkpoint inhibitors and prognosis of advanced non-small cell lung cancer. Sun D, etal., Mol Med. 2020 Aug 13;26(1):78. doi: 10.1186/s10020-020-00208-9.
25. Arid1a Has Context-Dependent Oncogenic and Tumor Suppressor Functions in Liver Cancer. Sun X, etal., Cancer Cell. 2017 Nov 13;32(5):574-589.e6. doi: 10.1016/j.ccell.2017.10.007.
26. Decreased expression of the ARID1A gene is associated with poor prognosis in primary gastric cancer. Wang DD, etal., PLoS One. 2012;7(7):e40364. doi: 10.1371/journal.pone.0040364. Epub 2012 Jul 13.
27. Clinicopathologic and prognostic relevance of ARID1A protein loss in colorectal cancer. Wei XL, etal., World J Gastroenterol. 2014 Dec 28;20(48):18404-12. doi: 10.3748/wjg.v20.i48.18404.
28. NF-κB/miR-223-3p/ARID1A axis is involved in Helicobacter pylori CagA-induced gastric carcinogenesis and progression. Yang F, etal., Cell Death Dis. 2018 Jan 9;9(1):12. doi: 10.1038/s41419-017-0020-9.
29. Low expression of ARID1A correlates with poor prognosis in intrahepatic cholangiocarcinoma. Yang SZ, etal., World J Gastroenterol. 2016 Jul 7;22(25):5814-21. doi: 10.3748/wjg.v22.i25.5814.
30. Loss of ARID1A promotes proliferation, migration and invasion via the Akt signaling pathway in NPC. Yang Y, etal., Cancer Manag Res. 2019 May 29;11:4931-4946. doi: 10.2147/CMAR.S207329. eCollection 2019.
31. Loss of ARID1A induces a stemness gene ALDH1A1 expression with histone acetylation in the malignant subtype of cholangiocarcinoma. Yoshino J, etal., Carcinogenesis. 2020 Jul 10;41(6):734-742. doi: 10.1093/carcin/bgz179.
32. Chromatin remodeling gene AT-rich interactive domain-containing protein 1A suppresses gastric cancer cell proliferation by targeting PIK3CA and PDK1. Zhang Q, etal., Oncotarget. 2016 Jul 19;7(29):46127-46141. doi: 10.18632/oncotarget.10060.
33. [Expression and clinical significance of ARID1A in gastric cancer and paired adjacent noncancerous tissues]. Zhang X, etal., Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi. 2017 Jan;33(1):77-80.
34. ARID1A is downregulated in non-small cell lung cancer and regulates cell proliferation and apoptosis. Zhang Y, etal., Tumour Biol. 2014 Jun;35(6):5701-7. doi: 10.1007/s13277-014-1755-x. Epub 2014 Feb 26.
35. The Clinicopathologic Significance of BAF250a (ARID1A) Expression in Hepatocellular Carcinoma. Zhao J, etal., Pathol Oncol Res. 2016 Jul;22(3):453-9. doi: 10.1007/s12253-015-0022-9. Epub 2015 Nov 20.
36. Expression and significance of EBV, ARID1A and PIK3CA in gastric carcinoma. Zhou H, etal., Mol Med Rep. 2019 Mar;19(3):2125-2136. doi: 10.3892/mmr.2019.9886. Epub 2019 Jan 22.
37. Loss of ARID1A expression is associated with poor prognosis in patients with gastric cancer. Zhu YP, etal., Hum Pathol. 2018 Aug;78:28-35. doi: 10.1016/j.humpath.2018.04.003. Epub 2018 Apr 22.
Additional References at PubMed
PMID:8804307   PMID:8895581   PMID:11078522   PMID:11318604   PMID:11726552   PMID:12200431   PMID:12368262   PMID:16287714   PMID:17363140   PMID:17640523   PMID:18448678   PMID:23129809  
PMID:23716698   PMID:23785148   PMID:24293408   PMID:24335282   PMID:31505169  


Genomics

Comparative Map Data
Arid1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25145,908,181 - 145,981,609 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5145,908,181 - 145,985,564 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5148,610,576 - 148,683,764 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.05150,380,181 - 150,453,373 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.05150,366,738 - 150,439,933 (-)NCBIRnor_WKY
Rnor_6.05151,904,687 - 151,977,973 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5151,904,684 - 151,977,636 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05155,592,617 - 155,665,889 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45151,355,617 - 151,398,647 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15151,335,330 - 151,408,688 (+)NCBI
Celera5144,329,185 - 144,372,216 (-)NCBICelera
Cytogenetic Map5q36NCBI
ARID1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38126,696,015 - 26,782,104 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl126,693,236 - 26,782,104 (+)EnsemblGRCh38hg38GRCh38
GRCh37127,022,506 - 27,108,595 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36126,895,109 - 26,981,188 (+)NCBINCBI36Build 36hg18NCBI36
Build 34126,706,666 - 26,792,737NCBI
Celera125,419,777 - 25,505,606 (+)NCBICelera
Cytogenetic Map1p36.11NCBI
HuRef125,309,350 - 25,361,809 (+)NCBIHuRef
CHM1_1127,135,825 - 27,221,852 (+)NCBICHM1_1
T2T-CHM13v2.0126,533,960 - 26,620,059 (+)NCBIT2T-CHM13v2.0
Arid1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394133,406,319 - 133,484,682 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4133,406,319 - 133,484,080 (-)EnsemblGRCm39 Ensembl
GRCm384133,679,008 - 133,756,769 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4133,679,008 - 133,756,769 (-)EnsemblGRCm38mm10GRCm38
MGSCv374133,234,923 - 133,309,526 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364132,951,084 - 133,029,633 (-)NCBIMGSCv36mm8
Celera4131,854,780 - 131,931,113 (-)NCBICelera
Cytogenetic Map4D2.3NCBI
Arid1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554526,068,631 - 6,120,759 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554526,068,631 - 6,120,759 (+)NCBIChiLan1.0ChiLan1.0
ARID1A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1127,019,596 - 27,103,239 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl127,018,616 - 27,103,239 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0125,960,868 - 26,047,057 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
ARID1A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1273,331,606 - 73,401,151 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl273,324,852 - 73,401,102 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha269,909,026 - 69,978,542 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0273,894,794 - 73,964,327 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl273,895,984 - 73,965,235 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1270,719,680 - 70,789,191 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0271,725,226 - 71,794,735 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0272,728,646 - 72,798,165 (-)NCBIUU_Cfam_GSD_1.0
Arid1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505845,325,365 - 45,372,530 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493647411,148,857 - 11,197,312 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ARID1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl684,049,087 - 84,123,349 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1684,049,729 - 84,124,302 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2677,607,507 - 77,623,800 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ARID1A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120105,981,549 - 106,066,093 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl20105,981,290 - 106,065,672 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603310,365,063 - 10,448,898 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Arid1a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476410,672,735 - 10,759,634 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476410,672,673 - 10,759,634 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Arid1a
127 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:532
Count of miRNA genes:260
Interacting mature miRNAs:323
Transcripts:ENSRNOT00000009173
Prediction methods:Microtar, Miranda, 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
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)597059760147465714Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)599216724148607142Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5103689353148689353Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5105999803150999803Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5106906205151906205Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5106906205151906205Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5106906205151906205Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5106906205151906205Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5106906205151906205Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5108845856153845856Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5108845856153845856Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)5108938288153938288Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5111416838156416838Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5111416838156416838Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5111416838156416838Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5111416838156416838Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5120740824151018848Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5129132447151006154Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132717196165560427Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5143069996166846814Rat
2302369Scl60Serum cholesterol level QTL 603.13blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)5143608201161165651Rat
631263Cm24Cardiac mass QTL 243.5heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)5143799107158428037Rat
1300119Bp180Blood pressure QTL 1803.82arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5144358090157869054Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5144377876161317411Rat

Markers in Region
RH143105  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25145,963,694 - 145,963,869 (+)MAPPERmRatBN7.2
Rnor_6.05151,960,413 - 151,960,587NCBIRnor6.0
Rnor_5.05155,648,343 - 155,648,517UniSTSRnor5.0
RGSC_v3.45151,342,970 - 151,343,144UniSTSRGSC3.4
Celera5144,384,690 - 144,384,864UniSTS
RH 3.4 Map5977.9UniSTS
Cytogenetic Map5q36UniSTS
RH143917  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25145,949,944 - 145,951,145 (+)MAPPERmRatBN7.2
Rnor_6.05151,946,450 - 151,947,650NCBIRnor6.0
Rnor_5.05155,634,380 - 155,635,580UniSTSRnor5.0
RGSC_v3.45151,355,686 - 151,356,886UniSTSRGSC3.4
Celera5144,370,947 - 144,372,147UniSTS
RH 3.4 Map14408.89UniSTS
Cytogenetic Map5q36UniSTS
AA818481  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25145,908,878 - 145,909,092 (+)MAPPERmRatBN7.2
Rnor_6.05151,905,387 - 151,905,600NCBIRnor6.0
Rnor_5.05155,593,317 - 155,593,530UniSTSRnor5.0
RGSC_v3.45151,397,736 - 151,397,949UniSTSRGSC3.4
Celera5144,329,883 - 144,330,096UniSTS
RH 3.4 Map5977.8UniSTS
Cytogenetic Map5q36UniSTS
MARC_6181-6182:992006984:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25145,909,189 - 145,909,581 (+)MAPPERmRatBN7.2
Rnor_6.05151,905,698 - 151,906,089NCBIRnor6.0
Rnor_5.05155,593,628 - 155,594,019UniSTSRnor5.0
RGSC_v3.45151,397,247 - 151,397,638UniSTSRGSC3.4
Celera5144,330,194 - 144,330,585UniSTS
Cytogenetic Map5q36UniSTS
MARC_11851-11852:1029349291:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25145,909,955 - 145,910,356 (+)MAPPERmRatBN7.2
Rnor_6.05151,906,464 - 151,906,864NCBIRnor6.0
Rnor_5.05155,594,394 - 155,594,794UniSTSRnor5.0
RGSC_v3.45151,396,472 - 151,396,872UniSTSRGSC3.4
Celera5144,330,960 - 144,331,360UniSTS
Cytogenetic Map5q36UniSTS


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 34 50 34 19 34 1 3 72 35 41 11 1
Low 9 7 7 7 7 8 2 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009173   ⟹   ENSRNOP00000009173
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5145,908,181 - 145,985,564 (-)Ensembl
Rnor_6.0 Ensembl5151,904,684 - 151,977,636 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102003   ⟹   ENSRNOP00000088707
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5145,908,181 - 145,985,564 (-)Ensembl
RefSeq Acc Id: NM_001106635   ⟹   NP_001100105
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25145,908,181 - 145,951,214 (-)NCBI
Rnor_6.05151,904,689 - 151,947,719 (-)NCBI
Rnor_5.05155,592,617 - 155,665,889 (-)NCBI
RGSC_v3.45151,355,617 - 151,398,647 (+)RGD
Celera5144,329,185 - 144,372,216 (-)RGD
Sequence:
RefSeq Acc Id: XM_006239011   ⟹   XP_006239073
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25145,908,845 - 145,981,178 (-)NCBI
Rnor_6.05151,904,687 - 151,977,973 (-)NCBI
Rnor_5.05155,592,617 - 155,665,889 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006239012   ⟹   XP_006239074
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25145,908,812 - 145,981,609 (-)NCBI
Rnor_6.05151,904,802 - 151,977,973 (-)NCBI
Rnor_5.05155,592,617 - 155,665,889 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039109412   ⟹   XP_038965340
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25145,915,052 - 145,981,178 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001100105   ⟸   NM_001106635
- Sequence:
RefSeq Acc Id: XP_006239074   ⟸   XM_006239012
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006239073   ⟸   XM_006239011
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000009173   ⟸   ENSRNOT00000009173
RefSeq Acc Id: XP_038965340   ⟸   XM_039109412
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000088707   ⟸   ENSRNOT00000102003
Protein Domains
ARID

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A3E3-F1-model_v2 AlphaFold D4A3E3 1-2021 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310500 AgrOrtholog
BioCyc Gene G2FUF-39619 BioCyc
Ensembl Genes ENSRNOG00000006137 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009173 ENTREZGENE
  ENSRNOP00000009173.7 UniProtKB/TrEMBL
  ENSRNOP00000088707 ENTREZGENE
  ENSRNOP00000088707.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009173 ENTREZGENE
  ENSRNOT00000009173.8 UniProtKB/TrEMBL
  ENSRNOT00000102003 ENTREZGENE
  ENSRNOT00000102003.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.60 UniProtKB/TrEMBL
  1.25.10.10 UniProtKB/TrEMBL
InterPro ARID/BRIGHT_DNA-bd UniProtKB/TrEMBL
  ARID_dom_sf UniProtKB/TrEMBL
  ARM-like UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/TrEMBL
  BAF250_C UniProtKB/TrEMBL
  BAF250a UniProtKB/TrEMBL
  DUF3518 UniProtKB/TrEMBL
NCBI Gene 297867 ENTREZGENE
PANTHER PTHR12656 UniProtKB/TrEMBL
  PTHR12656:SF12 UniProtKB/TrEMBL
Pfam ARID UniProtKB/TrEMBL
  DUF3518 UniProtKB/TrEMBL
PhenoGen Arid1a PhenoGen
PROSITE ARID UniProtKB/TrEMBL
SMART BRIGHT UniProtKB/TrEMBL
Superfamily-SCOP ARID UniProtKB/TrEMBL
  SSF48371 UniProtKB/TrEMBL
UniProt A0A8I6AJE2 ENTREZGENE, UniProtKB/TrEMBL
  D4A3E3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-25 Arid1a  AT-rich interaction domain 1A  Arid1a  AT rich interactive domain 1A (SWI-like)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Arid1a  AT rich interactive domain 1A (SWI-like)  Arid1a  AT rich interactive domain 1A (Swi1 like)   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Arid1a  AT rich interactive domain 1A (Swi1 like)   Arid1a_predicted  AT rich interactive domain 1A (Swi1 like) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Arid1a_predicted  AT rich interactive domain 1A (Swi1 like) (predicted)      Symbol and Name status set to approved 70820 APPROVED