Cab39 (calcium binding protein 39) - Rat Genome Database
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Gene: Cab39 (calcium binding protein 39) Rattus norvegicus
Analyze
Symbol: Cab39
Name: calcium binding protein 39
RGD ID: 1306390
Description: Predicted to have kinase binding activity and protein serine/threonine kinase activator activity. Involved in response to activity and response to thyroid hormone. Localizes to cytosol; membrane; and protein-containing complex. Colocalizes with Z disc. Biomarker of hyperthyroidism and transient cerebral ischemia. Human ortholog(s) of this gene implicated in hepatocellular carcinoma. Orthologous to human CAB39 (calcium binding protein 39); PARTICIPATES IN adenosine monophosphate-activated protein kinase (AMPK) signaling pathway; mTOR signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4,6-trinitrobenzenesulfonic acid; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: calcium-binding protein 39; LOC301574; MO25; MO25alpha
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
Rnor_6.0992,834,327 - 92,895,778 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl992,834,357 - 92,895,778 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0992,563,873 - 92,625,079 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4984,528,678 - 84,590,375 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1984,712,097 - 84,773,624 (+)NCBI
Celera983,885,355 - 83,945,864 (+)NCBICelera
Cytogenetic Map9q35NCBI
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

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:18854309   PMID:19056867   PMID:19199708   PMID:19892943   PMID:23376485   PMID:23533145   PMID:24393035   PMID:24811174  


Genomics

Comparative Map Data
Cab39
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0992,834,327 - 92,895,778 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl992,834,357 - 92,895,778 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0992,563,873 - 92,625,079 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4984,528,678 - 84,590,375 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1984,712,097 - 84,773,624 (+)NCBI
Celera983,885,355 - 83,945,864 (+)NCBICelera
Cytogenetic Map9q35NCBI
CAB39
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2230,712,842 - 230,821,075 (+)EnsemblGRCh38hg38GRCh38
GRCh382230,712,842 - 230,821,075 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372231,577,557 - 231,685,790 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362231,285,909 - 231,394,031 (+)NCBINCBI36hg18NCBI36
Build 342231,403,169 - 231,511,291NCBI
Celera2225,353,992 - 225,462,181 (+)NCBI
Cytogenetic Map2q37.1NCBI
HuRef2223,417,541 - 223,525,784 (+)NCBIHuRef
CHM1_12231,583,373 - 231,691,604 (+)NCBICHM1_1
Cab39
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39185,721,148 - 85,779,298 (+)NCBIGRCm39mm39
GRCm38185,793,441 - 85,851,577 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl185,793,441 - 85,851,576 (+)EnsemblGRCm38mm10GRCm38
MGSCv37187,690,022 - 87,748,152 (+)NCBIGRCm37mm9NCBIm37
MGSCv36187,626,534 - 87,681,536 (+)NCBImm8
Celera188,758,053 - 88,816,367 (+)NCBICelera
Cytogenetic Map1C5NCBI
Cab39
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554534,582,530 - 4,671,157 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554534,582,530 - 4,670,978 (-)NCBIChiLan1.0ChiLan1.0
CAB39
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B236,809,549 - 236,870,646 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B236,809,549 - 236,870,646 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B117,965,688 - 118,074,063 (+)NCBIMhudiblu_PPA_v0panPan3
CAB39
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2542,703,332 - 42,799,279 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12542,752,798 - 42,801,257 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Cab39
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365255,955,252 - 6,002,917 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CAB39
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15131,492,650 - 131,600,454 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115131,492,575 - 131,584,963 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CAB39
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110116,749,173 - 116,860,814 (+)NCBI
ChlSab1.1 Ensembl10116,798,825 - 116,861,332 (+)Ensembl
Cab39
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248434,129,755 - 4,217,406 (+)NCBI

Position Markers
AA960512  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0992,895,556 - 92,895,741NCBIRnor6.0
Rnor_6.0197,945,565 - 97,945,748NCBIRnor6.0
Rnor_5.0992,624,857 - 92,625,042UniSTSRnor5.0
Rnor_5.0199,027,336 - 99,027,519UniSTSRnor5.0
RGSC_v3.4984,590,153 - 84,590,338UniSTSRGSC3.4
RGSC_v3.4192,777,751 - 92,777,934UniSTSRGSC3.4
Celera187,223,205 - 87,223,388UniSTS
Celera983,945,642 - 83,945,827UniSTS
Cytogenetic Map9q35UniSTS
RH128526  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0992,895,554 - 92,895,751NCBIRnor6.0
Rnor_6.0197,945,563 - 97,945,758NCBIRnor6.0
Rnor_5.0992,624,855 - 92,625,052UniSTSRnor5.0
Rnor_5.0199,027,334 - 99,027,529UniSTSRnor5.0
RGSC_v3.4984,590,151 - 84,590,348UniSTSRGSC3.4
RGSC_v3.4192,777,749 - 92,777,944UniSTSRGSC3.4
Celera187,223,203 - 87,223,398UniSTS
Celera983,945,640 - 83,945,837UniSTS
Cytogenetic Map9q35UniSTS
RH131919  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0992,893,732 - 92,893,925NCBIRnor6.0
Rnor_5.0992,623,033 - 92,623,226UniSTSRnor5.0
RGSC_v3.4984,588,329 - 84,588,522UniSTSRGSC3.4
Celera983,943,818 - 83,944,011UniSTS
Cytogenetic Map9q35UniSTS
RH139163  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0992,856,425 - 92,856,573NCBIRnor6.0
Rnor_5.0992,585,941 - 92,586,089UniSTSRnor5.0
RGSC_v3.4984,550,746 - 84,550,894UniSTSRGSC3.4
Celera983,907,421 - 83,907,569UniSTS
Cytogenetic Map9q35UniSTS
UniSTS:234167  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0992,895,557 - 92,895,748NCBIRnor6.0
Rnor_6.0150,205,621 - 50,205,805NCBIRnor6.0
Rnor_5.0992,624,858 - 92,625,049UniSTSRnor5.0
Rnor_5.0149,548,684 - 49,548,868UniSTSRnor5.0
RGSC_v3.4984,590,154 - 84,590,345UniSTSRGSC3.4
RGSC_v3.4144,515,813 - 44,515,997UniSTSRGSC3.4
Celera983,945,643 - 83,945,834UniSTS
Celera145,805,255 - 45,805,439UniSTS
Cytogenetic Map1q11UniSTS
Cytogenetic Map9q35UniSTS
fk33e12.x1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0992,892,533 - 92,893,354NCBIRnor6.0
Rnor_5.0992,621,834 - 92,622,655UniSTSRnor5.0
RGSC_v3.4984,587,130 - 84,587,951UniSTSRGSC3.4
Celera983,942,619 - 83,943,440UniSTS
Cytogenetic Map9q35UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95417754299177542Rat
4889852Pur26Proteinuria QTL 26150.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)990024661107199079Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)99274129798606834Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)990024661119983851Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94126103498606834Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94724896594124663Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)966757444112943287Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)981411073119983851Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96745166499920892Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96745166499920892Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)970241351115241351Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)963270073107878387Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)98368615398164303Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)98368615398164303Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)98368615398164303Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)970942881115942881Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)983686153111609081Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)961186278106186278Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:380
Count of miRNA genes:214
Interacting mature miRNAs:280
Transcripts:ENSRNOT00000066440
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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001106924 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006245373 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006245374 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006245375 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596380 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07068249 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01061272 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01061273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01061274 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474004 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215375 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224987 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225203 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225560 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226825 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227560 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232683 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233663 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234937 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235111 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235215 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000066440   ⟹   ENSRNOP00000060020
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl992,834,357 - 92,895,778 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000085332   ⟹   ENSRNOP00000071044
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl992,859,988 - 92,893,614 (+)Ensembl
RefSeq Acc Id: NM_001106924   ⟹   NP_001100394
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0992,834,357 - 92,895,778 (+)NCBI
Rnor_5.0992,563,873 - 92,625,079 (+)NCBI
RGSC_v3.4984,528,678 - 84,590,375 (+)RGD
Celera983,885,355 - 83,945,864 (+)RGD
Sequence:
RefSeq Acc Id: XM_006245373   ⟹   XP_006245435
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0992,834,327 - 92,893,947 (+)NCBI
Rnor_5.0992,563,873 - 92,625,079 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006245374   ⟹   XP_006245436
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0992,835,512 - 92,893,947 (+)NCBI
Rnor_5.0992,563,873 - 92,625,079 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006245375   ⟹   XP_006245437
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0992,835,155 - 92,893,947 (+)NCBI
Rnor_5.0992,563,873 - 92,625,079 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596380   ⟹   XP_017451869
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0992,860,030 - 92,895,778 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001100394   ⟸   NM_001106924
- UniProtKB: D3ZJ77 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245435   ⟸   XM_006245373
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JZH0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245437   ⟸   XM_006245375
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JZH0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245436   ⟸   XM_006245374
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JZH0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451869   ⟸   XM_017596380
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JZH0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071044   ⟸   ENSRNOT00000085332
RefSeq Acc Id: ENSRNOP00000060020   ⟸   ENSRNOT00000066440

Transcriptome

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

Promoters
RGD ID:13696816
Promoter ID:EPDNEW_R7341
Type:initiation region
Name:Cab39_1
Description:calcium binding protein 39
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_6.0992,834,343 - 92,834,403EPDNEW

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)
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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

Database Acc Id Source(s)
AGR Gene RGD:1306390 AgrOrtholog
Ensembl Genes ENSRNOG00000017297 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000060020 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071044 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066440 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000085332 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/TrEMBL
InterPro ARM-like UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/TrEMBL
  Mo25 UniProtKB/TrEMBL
KEGG Report rno:301574 UniProtKB/TrEMBL
NCBI Gene 301574 ENTREZGENE
PANTHER PTHR10182 UniProtKB/TrEMBL
Pfam Mo25 UniProtKB/TrEMBL
PhenoGen Cab39 PhenoGen
Superfamily-SCOP ARM-type_fold UniProtKB/TrEMBL
UniGene Rn.103055 ENTREZGENE
UniProt A0A0G2JZH0 ENTREZGENE, UniProtKB/TrEMBL
  D3ZJ77 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Cab39  calcium binding protein 39   Cab39_predicted  calcium binding protein 39 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Cab39_predicted  calcium binding protein 39 (predicted)      Symbol and Name status set to approved 70820 APPROVED