Cadm2 (cell adhesion molecule 2) - Rat Genome Database
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Gene: Cadm2 (cell adhesion molecule 2) Rattus norvegicus
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Symbol: Cadm2
Name: cell adhesion molecule 2
RGD ID: 1305678
Description: Involved in brain development. Localizes to axon; cytoplasm; and neuronal cell body membrane. Human ortholog(s) of this gene implicated in astrocytoma; autism spectrum disorder; obesity; psoriasis; and type 2 diabetes mellitus. Orthologous to human CADM2 (cell adhesion molecule 2); INTERACTS WITH 1,2-dimethylhydrazine; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Igsf4d; immunoglobulin superfamily member 4D; immunoglobulin superfamily, member 4; LOC360687; Necl-3; nectin-like protein 3; synaptic cell adhesion molecule 2; SynCAM 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Cadm2Tn(sb-T2/Bart3)2.180Mcwi  
Genetic Models: F344-Cadm2Tn(sb-T2/Bart3)2.180Mcwi
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0114,175,078 - 4,397,335 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl114,174,881 - 4,397,361 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0117,871,257 - 8,090,100 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4114,273,771 - 5,330,393 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1114,273,770 - 4,503,107 (-)NCBI
Celera114,517,639 - 5,495,475 (-)NCBICelera
Cytogenetic Map11p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function
protein binding  (IPI,ISO)

References

Additional References at PubMed
PMID:22871113   PMID:29039453  


Genomics

Comparative Map Data
Cadm2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0114,175,078 - 4,397,335 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl114,174,881 - 4,397,361 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0117,871,257 - 8,090,100 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4114,273,771 - 5,330,393 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1114,273,770 - 4,503,107 (-)NCBI
Celera114,517,639 - 5,495,475 (-)NCBICelera
Cytogenetic Map11p12NCBI
CADM2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl384,958,981 - 86,074,429 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl384,958,989 - 86,074,429 (+)EnsemblGRCh38hg38GRCh38
GRCh38384,958,989 - 86,074,429 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37385,008,133 - 86,123,579 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36385,858,322 - 86,200,641 (+)NCBINCBI36hg18NCBI36
Build 34385,858,321 - 86,200,638NCBI
Celera385,754,715 - 86,870,332 (+)NCBI
Cytogenetic Map3p12.1NCBI
HuRef385,021,486 - 86,137,517 (+)NCBIHuRef
CHM1_1384,960,228 - 86,075,698 (+)NCBICHM1_1
Cadm2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391666,452,302 - 67,417,825 (-)NCBIGRCm39mm39
GRCm381666,655,416 - 67,620,917 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1666,655,421 - 67,620,908 (-)EnsemblGRCm38mm10GRCm38
MGSCv371666,655,666 - 67,621,153 (-)NCBIGRCm37mm9NCBIm37
MGSCv361666,579,334 - 67,539,146 (-)NCBImm8
Celera1666,933,305 - 67,895,289 (-)NCBICelera
Cytogenetic Map16C1.3- C2NCBI
Cadm2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554077,077,887 - 7,355,853 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554077,070,355 - 7,355,841 (-)NCBIChiLan1.0ChiLan1.0
CADM2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1387,200,283 - 88,318,087 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl387,200,482 - 88,310,438 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0385,076,738 - 86,200,515 (+)NCBIMhudiblu_PPA_v0panPan3
CADM2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl311,879,585 - 2,931,452 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1311,872,005 - 2,931,942 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Cadm2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366103,304,556 - 4,297,745 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CADM2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13169,688,940 - 170,752,425 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113169,681,947 - 170,753,114 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213180,745,385 - 180,922,682 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CADM2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12290,879,537 - 91,994,144 (-)NCBI
Cadm2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247891,245,224 - 2,316,519 (+)NCBI

Position Markers
D11Got5  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01112,960,913 - 12,961,148NCBIRnor6.0
Rnor_5.01116,620,702 - 16,620,937UniSTSRnor5.0
RGSC_v3.4114,815,880 - 4,816,115UniSTSRGSC3.4
RGSC_v3.4114,815,879 - 4,816,115RGDRGSC3.4
RGSC_v3.1114,815,880 - 4,816,115RGD
Celera115,066,743 - 5,066,978UniSTS
Cytogenetic Map11p12UniSTS
RH 3.4 Map110.0UniSTS
RH 3.4 Map110.0RGD
RH 2.0 Map11775.5RGD
D11Got1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01112,960,952 - 12,961,135NCBIRnor6.0
Rnor_5.01116,620,741 - 16,620,924UniSTSRnor5.0
RGSC_v3.4114,815,918 - 4,816,102RGDRGSC3.4
RGSC_v3.4114,815,919 - 4,816,102UniSTSRGSC3.4
RGSC_v3.1114,815,918 - 4,816,102RGD
Celera115,066,782 - 5,066,965UniSTS
Cytogenetic Map11p12UniSTS
RH 2.0 Map11803.6RGD
D11Mco8  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0114,349,717 - 4,349,963NCBIRnor6.0
Rnor_5.0118,043,362 - 8,043,608UniSTSRnor5.0
Celera114,701,802 - 4,702,048UniSTS
Cytogenetic Map11p12UniSTS
BF386655  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0114,188,829 - 4,189,003NCBIRnor6.0
Rnor_5.0117,885,091 - 7,885,265UniSTSRnor5.0
RGSC_v3.4114,288,166 - 4,288,340UniSTSRGSC3.4
Celera114,543,279 - 4,543,453UniSTS
Cytogenetic Map11p12UniSTS
BF387017  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01112,760,789 - 12,760,969NCBIRnor6.0
Rnor_5.01116,421,247 - 16,421,427UniSTSRnor5.0
RGSC_v3.4114,628,760 - 4,628,940UniSTSRGSC3.4
Celera114,880,105 - 4,880,285UniSTS
Cytogenetic Map11p12UniSTS
BF387497  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01113,346,949 - 13,347,098NCBIRnor6.0
Rnor_5.01117,000,642 - 17,000,791UniSTSRnor5.0
RGSC_v3.4115,277,567 - 5,277,716UniSTSRGSC3.4
Celera115,444,945 - 5,445,094UniSTS
Cytogenetic Map11p12UniSTS
AU047486  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera115,443,105 - 5,443,379UniSTS
Cytogenetic Map11p12UniSTS
RH137821  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01112,824,848 - 12,824,969NCBIRnor6.0
Rnor_5.01116,484,637 - 16,484,758UniSTSRnor5.0
RGSC_v3.4114,680,219 - 4,680,340UniSTSRGSC3.4
Celera114,931,153 - 4,931,274UniSTS
Cytogenetic Map11p12UniSTS
AU048452  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0114,280,946 - 4,281,119NCBIRnor6.0
Rnor_5.0117,977,193 - 7,977,366UniSTSRnor5.0
RGSC_v3.4114,383,860 - 4,384,033UniSTSRGSC3.4
Celera114,635,599 - 4,635,772UniSTS
Cytogenetic Map11p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11133867429Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11172720192Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)1132503169342559Rat


Genetic Models
This gene Cadm2 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:157
Count of miRNA genes:125
Interacting mature miRNAs:131
Transcripts:ENSRNOT00000046370
Prediction methods:Microtar, Miranda, 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
Medium 58 4
Low 1 20 6 1 1 1 14 10 25 6 1
Below cutoff 2 21 20 10 18 10 7 9 2 24 11 4 7

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001047102 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07033068 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07033069 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07033070 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067253 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067254 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067255 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067256 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067257 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067259 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067260 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067261 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067262 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067263 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067264 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067265 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067266 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067267 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067268 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067269 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067270 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067271 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067272 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067274 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067275 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067276 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067278 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067279 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067280 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067281 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067282 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067283 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01067284 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474018 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ272744 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000046370   ⟹   ENSRNOP00000040899
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl114,175,078 - 4,397,361 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000087133   ⟹   ENSRNOP00000073563
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl114,174,881 - 4,332,255 (-)Ensembl
RefSeq Acc Id: NM_001047102   ⟹   NP_001040567
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0114,175,078 - 4,397,335 (-)NCBI
Rnor_5.0117,871,257 - 8,090,100 (-)NCBI
RGSC_v3.4114,273,771 - 5,330,393 (-)RGD
Celera114,517,639 - 5,495,475 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001040567 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein ABB85363 (Get FASTA)   NCBI Sequence Viewer  
  EDL75913 (Get FASTA)   NCBI Sequence Viewer  
  Q1WIM2 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001040567   ⟸   NM_001047102
- Peptide Label: precursor
- UniProtKB: Q1WIM2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073563   ⟸   ENSRNOT00000087133
RefSeq Acc Id: ENSRNOP00000040899   ⟸   ENSRNOT00000046370
Protein Domains
Ig-like   Ig-like C2-type   Ig-like V-type

Transcriptome

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


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)
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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)
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:1305678 AgrOrtholog
Ensembl Genes ENSRNOG00000030840 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000040899 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073563 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000046370 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000087133 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CD80_C2-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_V-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neurexin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:360687 UniProtKB/Swiss-Prot
NCBI Gene 360687 ENTREZGENE
Pfam C2-set_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  V-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cadm2 PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART 4.1m UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IGc2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.202778 ENTREZGENE
UniProt A0A0A0MY16_RAT UniProtKB/TrEMBL
  A0A0G2K5U6_RAT UniProtKB/TrEMBL
  CADM2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-04 Cadm2  cell adhesion molecule 2  Igsf4d_predicted  immunoglobulin superfamily, member 4 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Igsf4d_predicted  immunoglobulin superfamily, member 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED