Ncam2 (neural cell adhesion molecule 2) - Rat Genome Database

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Gene: Ncam2 (neural cell adhesion molecule 2) Rattus norvegicus
Analyze
Symbol: Ncam2
Name: neural cell adhesion molecule 2
RGD ID: 1303131
Description: Predicted to have identical protein binding activity. Involved in axonal fasciculation and sensory perception of smell. Predicted to localize to axon; nuclear body; and plasma membrane. Orthologous to human NCAM2 (neural cell adhesion molecule 2); PARTICIPATES IN prion disease pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: fasciclin II; Ocam; OCAM-GPI
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
mRatBN7.21120,104,974 - 20,592,168 (+)NCBI
Rnor_6.0 Ensembl1120,471,764 - 20,705,063 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01119,669,922 - 20,705,063 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01123,856,942 - 24,353,041 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41120,409,948 - 20,911,422 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11120,423,191 - 20,911,422 (+)NCBI
Celera1119,468,505 - 20,502,763 (+)NCBICelera
Cytogenetic Map11q11NCBI
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

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:15677725   PMID:21300289  


Genomics

Comparative Map Data
Ncam2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21120,104,974 - 20,592,168 (+)NCBI
Rnor_6.0 Ensembl1120,471,764 - 20,705,063 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01119,669,922 - 20,705,063 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01123,856,942 - 24,353,041 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41120,409,948 - 20,911,422 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11120,423,191 - 20,911,422 (+)NCBI
Celera1119,468,505 - 20,502,763 (+)NCBICelera
Cytogenetic Map11q11NCBI
NCAM2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2120,998,409 - 21,543,329 (+)EnsemblGRCh38hg38GRCh38
GRCh382120,998,339 - 21,543,329 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372122,370,727 - 22,915,650 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362121,292,504 - 21,833,085 (+)NCBINCBI36hg18NCBI36
Build 342121,292,503 - 21,833,085NCBI
Celera217,541,720 - 8,085,871 (+)NCBI
Cytogenetic Map21q21.1NCBI
HuRef217,759,027 - 8,304,119 (+)NCBIHuRef
CHM1_12121,932,803 - 22,475,089 (+)NCBICHM1_1
Ncam2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391680,997,501 - 81,425,549 (+)NCBIGRCm39mm39
GRCm39 Ensembl1680,997,585 - 81,423,716 (+)Ensembl
GRCm381681,200,697 - 81,624,290 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1681,200,697 - 81,626,828 (+)EnsemblGRCm38mm10GRCm38
MGSCv371681,200,942 - 81,624,535 (+)NCBIGRCm37mm9NCBIm37
MGSCv361681,083,363 - 81,480,397 (+)NCBImm8
Celera1681,402,043 - 81,825,338 (+)NCBICelera
Cytogenetic Map16C3.3NCBI
cM Map1645.89NCBI
Ncam2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540721,730,434 - 22,215,377 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540721,730,331 - 22,220,664 (+)NCBIChiLan1.0ChiLan1.0
NCAM2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12121,061,757 - 21,602,254 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2121,344,602 - 21,601,438 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0217,703,278 - 8,250,763 (+)NCBIMhudiblu_PPA_v0panPan3
NCAM2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13116,912,768 - 17,434,854 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3116,912,908 - 17,429,510 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3116,950,212 - 17,475,661 (+)NCBI
ROS_Cfam_1.03116,954,178 - 17,471,017 (+)NCBI
UMICH_Zoey_3.13116,959,755 - 17,482,428 (+)NCBI
UNSW_CanFamBas_1.03116,972,239 - 17,488,890 (+)NCBI
UU_Cfam_GSD_1.03117,374,303 - 17,889,819 (+)NCBI
Ncam2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497118,126,187 - 18,346,662 (+)NCBI
SpeTri2.0NW_0049368221,033,660 - 1,189,131 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NCAM2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13185,176,885 - 185,679,885 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113185,176,282 - 185,679,891 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213195,314,227 - 195,518,758 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NCAM2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1271,075,834 - 71,622,707 (-)NCBI
ChlSab1.1 Ensembl271,076,654 - 71,442,031 (-)Ensembl
Ncam2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247459,327,125 - 9,826,922 (+)NCBI

Position Markers
RH130167  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21120,495,578 - 20,495,786 (+)MAPPER
mRatBN7.22183,061,435 - 183,061,643 (+)MAPPER
Rnor_6.01120,612,679 - 20,612,886NCBIRnor6.0
Rnor_6.02196,658,319 - 196,658,526NCBIRnor6.0
Rnor_5.01124,260,859 - 24,261,066UniSTSRnor5.0
Rnor_5.02216,157,018 - 216,157,225UniSTSRnor5.0
Cytogenetic Map11q11UniSTS
Cytogenetic Map2q34UniSTS
AU048257  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21120,260,896 - 20,261,026 (+)MAPPER
Rnor_6.01120,378,194 - 20,378,323NCBIRnor6.0
Rnor_5.01124,026,450 - 24,026,579UniSTSRnor5.0
RGSC_v3.41120,580,575 - 20,580,704UniSTSRGSC3.4
Celera1120,175,494 - 20,175,625UniSTS
Cytogenetic Map11q11UniSTS
NCAM2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21120,586,819 - 20,587,545 (+)MAPPER
Rnor_6.01120,703,613 - 20,704,338NCBIRnor6.0
Rnor_5.01124,351,591 - 24,352,316UniSTSRnor5.0
RGSC_v3.41120,909,972 - 20,910,697UniSTSRGSC3.4
Celera1120,501,313 - 20,502,038UniSTS
Cytogenetic Map11q11UniSTS


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
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11935127454351274Rat
2290451Scl58Serum cholesterol level QTL 583.48blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)111136730644444347Rat
724517Uae18Urinary albumin excretion QTL 183.7urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)111632197346583360Rat
1600394Edcs1Endometrial carcinoma susceptibility QTL12.90.04uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)111901627225069932Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111901627290463843Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)111947517979734728Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:462
Count of miRNA genes:253
Interacting mature miRNAs:302
Transcripts:ENSRNOT00000002895
Prediction methods:Microtar, Miranda, 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
Medium 56 4
Low 1 14 6 8 6 1 1 14 4 24 3 1
Below cutoff 2 35 28 20 11 20 7 8 4 22 13 6 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002895   ⟹   ENSRNOP00000002895
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1120,474,483 - 20,705,063 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078127   ⟹   ENSRNOP00000074294
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1120,471,764 - 20,703,553 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082417   ⟹   ENSRNOP00000074311
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1120,474,483 - 20,656,340 (+)Ensembl
RefSeq Acc Id: NM_203409   ⟹   NP_981954
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21120,105,003 - 20,591,984 (+)NCBI
Rnor_6.01119,669,922 - 20,705,063 (+)NCBI
Rnor_5.01123,856,942 - 24,353,041 (+)NCBI
RGSC_v3.41120,409,948 - 20,911,422 (+)RGD
Celera1119,468,505 - 20,502,763 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039088217   ⟹   XP_038944145
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21120,104,975 - 20,592,168 (+)NCBI
RefSeq Acc Id: XM_039088218   ⟹   XP_038944146
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21120,104,974 - 20,543,720 (+)NCBI
Protein Sequences
Protein RefSeqs NP_981954 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944145 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944146 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAS18425 (Get FASTA)   NCBI Sequence Viewer  
  AAS18426 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_981954   ⟸   NM_203409
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000074311   ⟸   ENSRNOT00000082417
RefSeq Acc Id: ENSRNOP00000002895   ⟸   ENSRNOT00000002895
RefSeq Acc Id: ENSRNOP00000074294   ⟸   ENSRNOT00000078127
RefSeq Acc Id: XP_038944146   ⟸   XM_039088218
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038944145   ⟸   XM_039088217
- Peptide Label: isoform X1
Protein Domains
Fibronectin type-III   Ig-like

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)
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)
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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

Database Acc Id Source(s)
AGR Gene RGD:1303131 AgrOrtholog
Ensembl Genes ENSRNOG00000002126 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002895 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074294 UniProtKB/TrEMBL
  ENSRNOP00000074311 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002895 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000078127 UniProtKB/TrEMBL
  ENSRNOT00000082417 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro FN3_sf UniProtKB/TrEMBL
  FN_III UniProtKB/TrEMBL
  Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_I-set UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/TrEMBL
  Ig_V-set UniProtKB/TrEMBL
  Neural_cell_adh UniProtKB/TrEMBL
KEGG Report rno:288280 UniProtKB/TrEMBL
NCBI Gene 288280 ENTREZGENE
Pfam fn3 UniProtKB/TrEMBL
  I-set UniProtKB/TrEMBL
PhenoGen Ncam2 PhenoGen
PRINTS NCAMFAMILY UniProtKB/TrEMBL
PROSITE FN3 UniProtKB/TrEMBL
  IG_LIKE UniProtKB/TrEMBL
SMART FN3 UniProtKB/TrEMBL
  IGc2 UniProtKB/TrEMBL
  IGv UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP FN_III-like UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A0G2K7P9_RAT UniProtKB/TrEMBL
  A0A0G2K7R3_RAT UniProtKB/TrEMBL
  F1M8G9_RAT UniProtKB/TrEMBL
  Q6RKB3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-02-14 Ncam2  neural cell adhesion molecule 2      Symbol and Name status set to provisional 70820 PROVISIONAL