Itm2b (integral membrane protein 2B) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Itm2b (integral membrane protein 2B) Rattus norvegicus
Analyze
Symbol: Itm2b
Name: integral membrane protein 2B
RGD ID: 620727
Description: Predicted to have ATP binding activity and amyloid-beta binding activity. Predicted to be involved in extrinsic apoptotic signaling pathway in absence of ligand and negative regulation of amyloid precursor protein biosynthetic process. Predicted to localize to several cellular components, including Golgi apparatus; Golgi-associated vesicle membrane; and integral component of organelle membrane. Human ortholog(s) of this gene implicated in ITM2B-related cerebral amyloid angiopathy 1 and ITM2B-related cerebral amyloid angiopathy 2. Orthologous to human ITM2B (integral membrane protein 2B); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Bri; imBRI2; immature BRI2; MGC94644; transmembrane protein BRI
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21548,545,998 - 48,568,904 (-)NCBI
Rnor_6.0 Ensembl1555,254,706 - 55,277,713 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01555,254,703 - 55,277,713 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01558,977,916 - 59,000,926 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41554,005,134 - 54,028,036 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11554,020,916 - 54,021,022 (-)NCBI
Celera1548,194,879 - 48,217,785 (-)NCBICelera
Cytogenetic Map15q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:10526337   PMID:10679242   PMID:12477932   PMID:15489334   PMID:16027166   PMID:17965014   PMID:18097506   PMID:18524908   PMID:19056867   PMID:19114711   PMID:19199708   PMID:19849849  
PMID:19946888   PMID:22194595   PMID:22871113   PMID:23376485   PMID:23533145   PMID:26515131   PMID:28176357  


Genomics

Comparative Map Data
Itm2b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21548,545,998 - 48,568,904 (-)NCBI
Rnor_6.0 Ensembl1555,254,706 - 55,277,713 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01555,254,703 - 55,277,713 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01558,977,916 - 59,000,926 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41554,005,134 - 54,028,036 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11554,020,916 - 54,021,022 (-)NCBI
Celera1548,194,879 - 48,217,785 (-)NCBICelera
Cytogenetic Map15q11NCBI
ITM2B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1348,232,612 - 48,270,357 (+)EnsemblGRCh38hg38GRCh38
GRCh381348,233,206 - 48,270,357 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371348,807,342 - 48,844,493 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361347,705,309 - 47,734,228 (+)NCBINCBI36hg18NCBI36
Build 341347,705,306 - 47,734,226NCBI
Celera1329,861,986 - 29,890,942 (+)NCBI
Cytogenetic Map13q14.2NCBI
HuRef1329,599,469 - 29,628,426 (+)NCBIHuRef
CHM1_11348,774,975 - 48,803,938 (+)NCBICHM1_1
Itm2b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391473,599,666 - 73,622,729 (-)NCBIGRCm39mm39
GRCm39 Ensembl1473,599,666 - 73,622,729 (-)Ensembl
GRCm381473,362,226 - 73,385,289 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1473,362,226 - 73,385,289 (-)EnsemblGRCm38mm10GRCm38
MGSCv371473,762,038 - 73,785,078 (-)NCBIGRCm37mm9NCBIm37
MGSCv361472,096,386 - 72,119,426 (-)NCBImm8
Celera1470,882,475 - 70,905,515 (-)NCBICelera
Cytogenetic Map14D3NCBI
cM Map1438.88NCBI
Itm2b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554311,928,706 - 1,937,238 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554311,928,706 - 1,935,010 (+)NCBIChiLan1.0ChiLan1.0
ITM2B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11348,105,762 - 48,113,838 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01329,383,318 - 29,412,018 (+)NCBIMhudiblu_PPA_v0panPan3
ITM2B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1223,255,139 - 3,261,440 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl223,255,631 - 3,261,433 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha223,283,458 - 3,311,398 (-)NCBI
ROS_Cfam_1.0223,368,494 - 3,396,449 (-)NCBI
UMICH_Zoey_3.1223,154,017 - 3,181,970 (-)NCBI
UNSW_CanFamBas_1.0223,216,709 - 3,244,525 (-)NCBI
UU_Cfam_GSD_1.0223,222,094 - 3,250,064 (-)NCBI
Itm2b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945158,051,536 - 158,073,617 (+)NCBI
SpeTri2.0NW_0049365651,535,570 - 1,557,667 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ITM2B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1119,349,133 - 19,377,917 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11119,349,088 - 19,377,931 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21119,802,615 - 19,874,829 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ITM2B
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1326,149,429 - 26,178,172 (+)NCBI
ChlSab1.1 Ensembl326,149,379 - 26,177,622 (+)Ensembl
Vero_WHO_p1.0NW_02366605717,730,923 - 17,759,981 (-)NCBI
Itm2b
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247486,598,986 - 6,622,679 (-)NCBI

Position Markers
RH142637  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21548,564,033 - 48,564,155 (+)MAPPER
Rnor_6.01555,272,842 - 55,272,963NCBIRnor6.0
Rnor_5.01558,996,055 - 58,996,176UniSTSRnor5.0
RGSC_v3.41554,023,166 - 54,023,287UniSTSRGSC3.4
Celera1548,212,915 - 48,213,036UniSTS
Cytogenetic Map15p11UniSTS
RH129302  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21548,546,649 - 48,546,829 (+)MAPPER
Rnor_6.01555,255,355 - 55,255,534NCBIRnor6.0
Rnor_5.01558,978,568 - 58,978,747UniSTSRnor5.0
RGSC_v3.41554,005,786 - 54,005,965UniSTSRGSC3.4
Celera1548,195,531 - 48,195,710UniSTS
Cytogenetic Map15p11UniSTS
RH142259  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21548,546,673 - 48,546,831 (+)MAPPER
Rnor_6.01555,255,379 - 55,255,536NCBIRnor6.0
Rnor_5.01558,978,592 - 58,978,749UniSTSRnor5.0
RGSC_v3.41554,005,810 - 54,005,967UniSTSRGSC3.4
Celera1548,195,555 - 48,195,712UniSTS
Cytogenetic Map15p11UniSTS
RH141160  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21548,546,414 - 48,546,597 (+)MAPPER
Rnor_6.01555,255,120 - 55,255,302NCBIRnor6.0
Rnor_5.01558,978,333 - 58,978,515UniSTSRnor5.0
RGSC_v3.41554,005,551 - 54,005,733UniSTSRGSC3.4
Celera1548,195,296 - 48,195,478UniSTS
Cytogenetic Map15p11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15162301382Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151071919155719191Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151549236072568189Rat
9590272Scort14Serum corticosterone level QTL 142.780.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)151698090761980907Rat
8694427Bw163Body weight QTL 1634.820.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)151698090761980907Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151724964162249641Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151809320881255430Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151851391388036354Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1526381041106550657Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1526381041106550657Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1526381041106550657Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152870974173709741Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)153321910189640841Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)153321910189640841Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)153321910189640841Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)153948079762596410Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153974955779033707Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153974955779033707Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)154106809486068094Rat
7411725Strs7Sensitivity to stroke QTL 73.8cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)154275724156027084Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1543097470106550657Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:122
Count of miRNA genes:91
Interacting mature miRNAs:107
Transcripts:ENSRNOT00000023037
Prediction methods: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.


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 4 13 3 2
Medium 3 43 57 41 19 41 8 11 70 22 38 9 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001006963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599637 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF034245 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC083735 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473951 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210227 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210419 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212539 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212626 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212795 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212925 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213415 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218718 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219378 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219414 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219676 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229426 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230065 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000272 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000023037   ⟹   ENSRNOP00000023037
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1555,254,706 - 55,277,713 (-)Ensembl
RefSeq Acc Id: NM_001006963   ⟹   NP_001006964
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21548,545,998 - 48,568,904 (-)NCBI
Rnor_6.01555,254,703 - 55,277,713 (-)NCBI
Rnor_5.01558,977,916 - 59,000,926 (-)NCBI
RGSC_v3.41554,005,134 - 54,028,036 (-)RGD
Celera1548,194,879 - 48,217,785 (-)RGD
Sequence:
RefSeq Acc Id: XM_017599637   ⟹   XP_017455126
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01555,254,703 - 55,268,728 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001006964 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH83735 (Get FASTA)   NCBI Sequence Viewer  
  EDM02268 (Get FASTA)   NCBI Sequence Viewer  
  Q5XIE8 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001006964   ⟸   NM_001006963
- UniProtKB: Q5XIE8 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017455126   ⟸   XM_017599637
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000023037   ⟸   ENSRNOT00000023037
Protein Domains
BRICHOS

Transcriptome

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

Promoters
RGD ID:13699823
Promoter ID:EPDNEW_R10347
Type:initiation region
Name:Itm2b_1
Description:integral membrane protein 2B
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_6.01555,277,709 - 55,277,769EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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

Database Acc Id Source(s)
AGR Gene RGD:620727 AgrOrtholog
Ensembl Genes ENSRNOG00000016271 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000023037 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000023037 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7191589 IMAGE-MGC_LOAD
InterPro BRICHOS_dom UniProtKB/Swiss-Prot
  ITM2 UniProtKB/Swiss-Prot
KEGG Report rno:290364 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94644 IMAGE-MGC_LOAD
NCBI Gene 290364 ENTREZGENE
PANTHER PTHR10962 UniProtKB/Swiss-Prot
Pfam BRICHOS UniProtKB/Swiss-Prot
PhenoGen Itm2b PhenoGen
PROSITE BRICHOS UniProtKB/Swiss-Prot
SMART BRICHOS UniProtKB/Swiss-Prot
UniProt ITM2B_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Itm2b  integral membrane protein 2B      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Itm2b  integral membrane protein 2B      Symbol and Name status set to provisional 70820 PROVISIONAL