Itm2a (integral membrane protein 2A)

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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 have amyloid-beta binding activity. Predicted to be involved in negative regulation of amyloid precursor protein biosynthetic process and plasma cell differentiation. Predicted to localize to Golgi apparatus and plasma membrane. 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

Also known as:

MGC116343

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	ITM2A (integral membrane protein 2A)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Itm2a (integral membrane protein 2A)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Itm2a (integral membrane protein 2A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	ITM2A (integral membrane protein 2A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Itm2a (integral membrane protein 2A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	ITM2A (integral membrane protein 2A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	ITM2A (integral membrane protein 2A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Itm2a (integral membrane protein 2A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	ITM2A (integral membrane protein 2A)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Itm2a (integral membrane protein 2A)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	C25F6.7	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	CG3662	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	X	72,486,383 - 72,492,344 (-)	NCBI
Rnor_6.0 Ensembl	X	78,490,866 - 78,496,847 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	X	78,490,872 - 78,496,814 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	X	78,689,825 - 78,695,767 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	95,637,901 - 95,643,845 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	X	73,777,451 - 73,783,344 (-)	NCBI		Celera
Cytogenetic Map	X	q22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autistic disorder (ISO)

COVID-19 (ISO)

syndromic X-linked intellectual disability Lubs type (ISO)

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)

2,4,6-trinitrobenzenesulfonic acid (ISO)

2,6-dinitrotoluene (EXP)

2-hydroxypropanoic acid (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

4,4'-sulfonyldiphenol (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

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)

carbon nanotube (ISO)

cisplatin (ISO)

curcumin (ISO)

dexamethasone (ISO)

diarsenic trioxide (ISO)

dibenz[a,h]anthracene (ISO)

diclofenac (ISO)

dioxygen (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

entinostat (ISO)

ethyl methanesulfonate (ISO)

folic acid (ISO)

formaldehyde (ISO)

indometacin (ISO)

mercury dibromide (ISO)

methamphetamine (EXP)

methotrexate (ISO)

methyl methanesulfonate (ISO)

methylmercury chloride (ISO)

monosodium L-glutamate (ISO)

nickel atom (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)

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

negative regulation of amyloid precursor protein biosynthetic process (IBA)

plasma cell differentiation (ISO)

Cellular Component

Golgi apparatus (IBA)

integral component of membrane (IEA)

plasma membrane (IBA)

Molecular Function

amyloid-beta binding (IBA)

protein binding (ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	RGD automated import pipeline for gene-chemical interactions
3.	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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	X	72,486,383 - 72,492,344 (-)	NCBI
Rnor_6.0 Ensembl	X	78,490,866 - 78,496,847 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	X	78,490,872 - 78,496,814 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	X	78,689,825 - 78,695,767 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	95,637,901 - 95,643,845 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	X	73,777,451 - 73,783,344 (-)	NCBI		Celera
Cytogenetic Map	X	q22	NCBI

ITM2A
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	X	79,360,384 - 79,367,667 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	X	79,360,384 - 79,367,334 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	X	78,615,881 - 78,622,831 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	X	78,502,537 - 78,509,703 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	X	78,422,027 - 78,428,949	NCBI
Celera	X	78,856,181 - 78,863,347 (-)	NCBI
Cytogenetic Map	X	q21.1	NCBI
HuRef	X	72,195,097 - 72,202,264 (-)	NCBI		HuRef
CHM1_1	X	78,509,045 - 78,516,210 (-)	NCBI		CHM1_1

Itm2a
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	X	106,440,801 - 106,446,966 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	X	106,440,705 - 106,446,982 (-)	Ensembl
GRCm38	X	107,397,195 - 107,403,360 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	X	107,397,099 - 107,403,376 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	X	104,592,534 - 104,598,699 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	X	103,599,914 - 103,606,079 (-)	NCBI			mm8
Celera	X	94,234,855 - 94,241,346 (-)	NCBI		Celera
Cytogenetic Map	X	D	NCBI

Itm2a
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955557	2,235,223 - 2,243,927 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955557	2,235,223 - 2,243,911 (-)	NCBI	ChiLan1.0	ChiLan1.0

ITM2A
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	X	78,585,836 - 78,593,037 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	X	78,585,836 - 78,593,037 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	X	68,475,114 - 68,482,274 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

Itm2a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	X	54,940,289 - 54,947,031 (-)	NCBI
SpeTri2.0	NW_004936547	1,260,705 - 1,267,443 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ITM2A
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	X	63,430,021 - 63,437,032 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	X	63,430,020 - 63,437,027 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	X	72,699,051 - 72,706,070 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

ITM2A
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	X	68,339,399 - 68,346,572 (-)	NCBI
ChlSab1.1 Ensembl	X	68,339,357 - 68,346,415 (-)	Ensembl

Itm2a
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624836	1,657,678 - 1,663,905 (+)	NCBI

Position Markers

AW108051

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	7	20,249,713 - 20,249,835 (+)	MAPPER
mRatBN7.2	X	72,486,433 - 72,486,572 (+)	MAPPER
Rnor_6.0	X	78,490,923 - 78,491,061	NCBI	Rnor6.0
Rnor_6.0	7	26,370,715 - 26,370,836	NCBI	Rnor6.0
Rnor_5.0	7	26,501,170 - 26,501,291	UniSTS	Rnor5.0
Rnor_5.0	X	78,689,876 - 78,690,014	UniSTS	Rnor5.0
RGSC_v3.4	X	95,637,952 - 95,638,090	UniSTS	RGSC3.4
RGSC_v3.4	7	22,393,467 - 22,393,588	UniSTS	RGSC3.4
Celera	7	17,451,870 - 17,451,991	UniSTS
Celera	X	73,777,502 - 73,777,640	UniSTS
Cytogenetic Map	X	q31	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
61430	Cia18	Collagen induced arthritis QTL 18	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	X	15688119	127888215	Rat
1598837	Memor13	Memory QTL 13	3.2		exploratory 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)	X	44320616	158345622	Rat
738035	Stresp1	Stress response QTL 1	4.96	0.000011	stress-related behavior trait (VT:0010451)	defensive burying - coping	X	44557974	120045269	Rat
61431	Cia19	Collagen induced arthritis QTL 19	4.4		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	X	70352120	127888215	Rat

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.

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											2
Medium		38	34	24	16	24	8	11	74	18	31	11	8
Low	3	5	22	16	3	16				17	8
Below cutoff			1	1		1

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001025712	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC099174	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473969	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ214824	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ216632	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ217144	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ224887	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000423	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000003265 ⟹ ENSRNOP00000003265

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	X	78,490,866 - 78,496,847 (-)	Ensembl

RefSeq Acc Id:

NM_001025712 ⟹ NP_001020883

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	X	72,486,383 - 72,492,344 (-)	NCBI
Rnor_6.0	X	78,490,872 - 78,496,814 (-)	NCBI
Rnor_5.0	X	78,689,825 - 78,695,767 (-)	NCBI
RGSC_v3.4	X	95,637,901 - 95,643,845 (-)	RGD
Celera	X	73,777,451 - 73,783,344 (-)	RGD

Sequence:

show sequence

GAGACAGTAAGTGCTGCTCAAGTAGCGCGATCCTCTCCTCTTCCAACCTGCAGCCCAAGCTACT
GATTCGAGCCGCGCCTTACCGCGCTGCCCGAAGATTCACCATGGTGAAGATCGCCTTCAACACC
CCCACGGCGGTGCAAAAGGAGGAGGCTCGGCAAGATGTGGAGGCACTCGTCAGCCGCACTGTCC
GAGCTCAAATCCTGACTGGCAAGGAGCTCAGAGTCGTCCCGCAGGAGAAAGATAGCTCGTCTGG
GAGATGTATGCTTACTCTCTTAGGCCTCTCGTTCATCTTGGCAGGACTGATTGTTGGTGGAGCC
TGCATTTATAAGTACTTCATGCCCAAGAGCACCATTTACCATGGTGAGATGTGCTTCTTTGACT
CTGAGGATGCTGTAAATTCCATTCATGGAGGACAGCCATACTTTCTGCCTGTGACTGAGGAAGC
CGATATTCGTGAGGATGACAACATCGCAATCATTGACGTGCCCGTTCCCAGTTTCTCCGACAGT
GACCCTGCGGCAATTATTCACGACTTTGAGAAGGGAATGACTGCTTACCTGGACTTGCTTTTGG
GAAACTGTTACCTGATGCCCCTCAACACTTCCATTGTGATGACTCCAAAGAATCTGGTGGAGCT
TTTTGGCAAACTGGCAAGTGGCAAGTATTTGCCTCATACTTATGTGGTTCGTGAAGACCTGGTT
GCTGTGGAAGAAATTCGTGATGTTAGTAACCTTGGTATTTTTATTTACCAACTTTGCAACAACC
GAAAGTCCTTCCGCCTTAGACGCAGAGACCTCCTGCTGGGTTTCAATAAGCGTGCCATTGACAA
ATGCTGGAAGATCAGACACTTCCCCAATGAATTCATCGTCGAAACCAAGATCTGTCAAGAGTGA
AGAGTGACAGATAAAGAGTATCCTTGGTAATAAGAAGTCAGAAACTTGCCGTCTGACTTTGATA
TTGAAATTGATGGGATACTCAAGCTATTTACCCATACATTTACTCCATTGCTTATACTGGAAAA
GGAAAGGGGGGAGAAAACTACTAACCACTGCAAGCGATTGTGCAATTCTAGTTCAATTGACATT
GCTTGCTGTTTTCAACAAATGAAATGATTATCTTTTCTCTTGAATTTATAGGGTTTAGATTTCT
GAAAGCAGCATGAATGTGTCATCTTACTCTCCTGACAAAAAATCCCATTCTCTGGTGTTATTTA
AAGCATGTTCTTAACAAAAATCATTTCATGCTTTAAATTGAAAATATTTGAAATTTGTTCTTGA
CATTTTTGTGTGAAGCATGTCAAAGCTCTTACCGTTCTCTTGTTTTCTTCTTCATTGTGTTCAA
CTCTCCTGATTTCAGAAGTTACATTTTTGCATTTCTATCAGGTGCTGTGTAACGAATCTGACTG
ATATGTGAACAATCTTCATGAGAAAGCAATTTTTTTACTCATGTAATGATTCTTTCTCACTGAT
ATCTGTATTGTGAAATCCACAGAACTGTACGGGTGCTGAATGCTGTAAGGAGCTCTGGTTGTAT
GAATTCTACAACCCTATAATAAAGTTTACCATATTCAAAAAAAAAAAAAAAAAAAAAAAAA

hide 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

Reference Sequences

RefSeq Acc Id:

NP_001020883 ⟸ NM_001025712

- UniProtKB:

Q4KLJ2 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MVKIAFNTPTAVQKEEARQDVEALVSRTVRAQILTGKELRVVPQEKDSSSGRCMLTLLGLSFIL
AGLIVGGACIYKYFMPKSTIYHGEMCFFDSEDAVNSIHGGQPYFLPVTEEADIREDDNIAIIDV
PVPSFSDSDPAAIIHDFEKGMTAYLDLLLGNCYLMPLNTSIVMTPKNLVELFGKLASGKYLPHT
YVVREDLVAVEEIRDVSNLGIFIYQLCNNRKSFRLRRRDLLLGFNKRAIDKCWKIRHFPNEFIV
ETKICQE

hide sequence

RefSeq Acc Id:

ENSRNOP00000003265 ⟸ ENSRNOT00000003265

Protein Domains

BRICHOS

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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	X	78,496,833 - 78,496,893	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

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CSV

TAB

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

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CSV

TAB

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1559423	AgrOrtholog
Ensembl Genes	ENSRNOG00000002365	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000003265	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000003265	ENTREZGENE, 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	PTHR10962	UniProtKB/TrEMBL
Pfam	BRICHOS	UniProtKB/TrEMBL
PhenoGen	Itm2a	PhenoGen
PROSITE	BRICHOS	UniProtKB/TrEMBL
SMART	BRICHOS	UniProtKB/TrEMBL
UniProt	Q4KLJ2	ENTREZGENE, 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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - ClinVar