Itm2a (integral membrane protein 2A) - Rat Genome Database

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Gene: Itm2a (integral membrane protein 2A) Rattus norvegicus
Analyze
Symbol: Itm2a
Name: integral membrane protein 2A
RGD ID: 1559423
Description: Predicted to act upstream of or within plasma cell differentiation. Orthologous to human ITM2A (integral membrane protein 2A); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: MGC116343
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X76,559,183 - 76,565,144 (-)NCBIGRCr8
mRatBN7.2X72,486,383 - 72,492,344 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX72,486,381 - 72,492,363 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX73,982,580 - 73,988,542 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X77,502,307 - 77,508,257 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X75,062,872 - 75,068,833 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X78,490,872 - 78,496,814 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX78,490,866 - 78,496,847 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X78,689,825 - 78,695,767 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X95,637,901 - 95,643,845 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX73,777,451 - 73,783,344 (-)NCBICelera
Cytogenetic MapXq22NCBI
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
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2,6-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-Nitrobenzanthrone  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
actinomycin D  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-Zearalanol  (EXP)
amitrole  (EXP)
antirheumatic drug  (ISO)
arsenous acid  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
beta-carotene  (ISO)
bexarotene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butanal  (ISO)
camptothecin  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
cisplatin  (ISO)
curcumin  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dibenzofurans  (ISO)
diclofenac  (ISO)
dimethylarsinic acid  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethyl methanesulfonate  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
gentamycin  (EXP)
indometacin  (ISO)
mercury dibromide  (ISO)
methamphetamine  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
monosodium L-glutamate  (ISO)
nickel atom  (ISO)
Nutlin-3  (ISO)
ozone  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
pentanal  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
phenylmercury acetate  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
propanal  (ISO)
rac-lactic acid  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sulfadimethoxine  (EXP)
sunitinib  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
tolcapone  (EXP)
trichostatin A  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. 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:22871113   PMID:24831988  


Genomics

Comparative Map Data
Itm2a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X76,559,183 - 76,565,144 (-)NCBIGRCr8
mRatBN7.2X72,486,383 - 72,492,344 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX72,486,381 - 72,492,363 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX73,982,580 - 73,988,542 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X77,502,307 - 77,508,257 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X75,062,872 - 75,068,833 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X78,490,872 - 78,496,814 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX78,490,866 - 78,496,847 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X78,689,825 - 78,695,767 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X95,637,901 - 95,643,845 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX73,777,451 - 73,783,344 (-)NCBICelera
Cytogenetic MapXq22NCBI
ITM2A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X79,360,384 - 79,367,334 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX79,360,384 - 79,367,667 (-)EnsemblGRCh38hg38GRCh38
GRCh37X78,615,881 - 78,622,831 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X78,502,537 - 78,509,703 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X78,422,027 - 78,428,949NCBI
CeleraX78,856,181 - 78,863,347 (-)NCBICelera
Cytogenetic MapXq21.1NCBI
HuRefX72,195,097 - 72,202,264 (-)NCBIHuRef
CHM1_1X78,509,045 - 78,516,210 (-)NCBICHM1_1
T2T-CHM13v2.0X77,797,066 - 77,804,015 (-)NCBIT2T-CHM13v2.0
Itm2a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X106,440,801 - 106,446,966 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX106,440,705 - 106,446,982 (-)EnsemblGRCm39 Ensembl
GRCm38X107,397,195 - 107,403,360 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX107,397,099 - 107,403,376 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X104,592,534 - 104,598,699 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X103,599,914 - 103,606,079 (-)NCBIMGSCv36mm8
CeleraX94,234,855 - 94,241,346 (-)NCBICelera
Cytogenetic MapXDNCBI
cM MapX47.52NCBI
Itm2a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555572,235,223 - 2,243,927 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555572,235,223 - 2,243,911 (-)NCBIChiLan1.0ChiLan1.0
ITM2A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X78,874,710 - 78,881,798 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X78,878,321 - 78,885,409 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X68,475,114 - 68,482,274 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X78,585,836 - 78,593,037 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX78,585,836 - 78,593,037 (-)Ensemblpanpan1.1panPan2
Itm2a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X54,940,289 - 54,947,031 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365471,260,696 - 1,267,618 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365471,260,705 - 1,267,443 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ITM2A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX63,430,021 - 63,437,032 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X63,430,020 - 63,437,027 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X72,699,051 - 72,706,070 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ITM2A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X68,339,399 - 68,346,572 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX68,339,357 - 68,346,415 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606713,006,174 - 13,013,388 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Itm2a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248361,657,568 - 1,664,297 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248361,657,678 - 1,663,905 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Itm2a
11 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:179
Count of miRNA genes:137
Interacting mature miRNAs:150
Transcripts:ENSRNOT00000003265
Prediction methods:Miranda, Pita, Rnahybrid
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
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat

Markers in Region
AW108051  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2720,249,713 - 20,249,835 (+)MAPPERmRatBN7.2
mRatBN7.2X72,486,433 - 72,486,572 (+)MAPPERmRatBN7.2
Rnor_6.0X78,490,923 - 78,491,061NCBIRnor6.0
Rnor_6.0726,370,715 - 26,370,836NCBIRnor6.0
Rnor_5.0726,501,170 - 26,501,291UniSTSRnor5.0
Rnor_5.0X78,689,876 - 78,690,014UniSTSRnor5.0
RGSC_v3.4X95,637,952 - 95,638,090UniSTSRGSC3.4
RGSC_v3.4722,393,467 - 22,393,588UniSTSRGSC3.4
Celera717,451,870 - 17,451,991UniSTS
CeleraX73,777,502 - 73,777,640UniSTS
Cytogenetic MapXq31UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000003265   ⟹   ENSRNOP00000003265
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX72,486,381 - 72,492,363 (-)Ensembl
Rnor_6.0 EnsemblX78,490,866 - 78,496,847 (-)Ensembl
RefSeq Acc Id: NM_001025712   ⟹   NP_001020883
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X76,559,183 - 76,565,144 (-)NCBI
mRatBN7.2X72,486,383 - 72,492,344 (-)NCBI
Rnor_6.0X78,490,872 - 78,496,814 (-)NCBI
Rnor_5.0X78,689,825 - 78,695,767 (-)NCBI
RGSC_v3.4X95,637,901 - 95,643,845 (-)RGD
CeleraX73,777,451 - 73,783,344 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001020883 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH99174 (Get FASTA)   NCBI Sequence Viewer  
  EDM07112 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000003265.4
RefSeq Acc Id: NP_001020883   ⟸   NM_001025712
- UniProtKB: Q4KLJ2 (UniProtKB/TrEMBL),   A6IV68 (UniProtKB/TrEMBL),   F7F6C1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000003265   ⟸   ENSRNOT00000003265
Protein Domains
BRICHOS

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4KLJ2-F1-model_v2 AlphaFold Q4KLJ2 1-263 view protein structure

Transcriptome

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

Promoters
RGD ID:13701906
Promoter ID:EPDNEW_R12430
Type:initiation region
Name:Itm2a_1
Description:integral membrane protein 2A
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_6.0X78,496,833 - 78,496,893EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559423 AgrOrtholog
BioCyc Gene G2FUF-1892 BioCyc
Ensembl Genes ENSRNOG00000002365 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003265.8 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7382658 IMAGE-MGC_LOAD
InterPro BRICHOS UniProtKB/TrEMBL
  ITM2 UniProtKB/TrEMBL
KEGG Report rno:317218 UniProtKB/TrEMBL
MGC_CLONE MGC:116343 IMAGE-MGC_LOAD
NCBI Gene 317218 ENTREZGENE
PANTHER INTEGRAL MEMBRANE PROTEIN 2A UniProtKB/TrEMBL
  PTHR10962 UniProtKB/TrEMBL
Pfam BRICHOS UniProtKB/TrEMBL
PhenoGen Itm2a PhenoGen
PROSITE BRICHOS UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002365 RatGTEx
SMART BRICHOS UniProtKB/TrEMBL
UniProt A6IV68 ENTREZGENE, UniProtKB/TrEMBL
  F7F6C1 ENTREZGENE, UniProtKB/TrEMBL
  Q4KLJ2 ENTREZGENE
UniProt Secondary Q4KLJ2 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Itm2a  integral membrane protein 2A      Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 Itm2a  integral membrane protein 2A      Symbol and Name status set to provisional 70820 PROVISIONAL