Boc (BOC cell adhesion associated, oncogene regulated) - Rat Genome Database
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Gene: Boc (BOC cell adhesion associated, oncogene regulated) Rattus norvegicus
Analyze
Symbol: Boc
Name: BOC cell adhesion associated, oncogene regulated
RGD ID: 1304550
Description: Predicted to be involved in axon guidance; positive regulation of myoblast differentiation; and smoothened signaling pathway. Localizes to axonal growth cone. Orthologous to human BOC (BOC cell adhesion associated, oncogene regulated); PARTICIPATES IN altered Hedgehog signaling pathway; Hedgehog signaling pathway; pancreatic cancer pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein; brother of CDO; LOC360715
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
mRatBN7.21156,122,697 - 56,198,060 (+)NCBI
Rnor_6.0 Ensembl1161,083,757 - 61,158,838 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01161,084,216 - 61,159,220 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01165,191,723 - 65,266,748 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41157,668,326 - 57,710,373 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11157,725,916 - 57,801,302 (+)NCBI
Celera1155,682,824 - 55,757,735 (+)NCBICelera
Cytogenetic Map11q21NCBI
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:8889548   PMID:11782431   PMID:12477932   PMID:16647303   PMID:17086203  


Genomics

Comparative Map Data
Boc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21156,122,697 - 56,198,060 (+)NCBI
Rnor_6.0 Ensembl1161,083,757 - 61,158,838 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01161,084,216 - 61,159,220 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01165,191,723 - 65,266,748 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41157,668,326 - 57,710,373 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11157,725,916 - 57,801,302 (+)NCBI
Celera1155,682,824 - 55,757,735 (+)NCBICelera
Cytogenetic Map11q21NCBI
BOC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3113,211,003 - 113,287,459 (+)EnsemblGRCh38hg38GRCh38
GRCh383113,211,003 - 113,287,463 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373112,930,404 - 113,006,306 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363114,414,065 - 114,488,996 (+)NCBINCBI36hg18NCBI36
Celera3111,339,962 - 111,414,896 (+)NCBI
Cytogenetic Map3q13.2NCBI
HuRef3110,306,382 - 110,381,047 (+)NCBIHuRef
CHM1_13112,893,912 - 112,969,893 (+)NCBICHM1_1
Boc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391644,305,408 - 44,379,233 (-)NCBIGRCm39mm39
GRCm39 Ensembl1644,305,412 - 44,379,260 (-)Ensembl
GRCm381644,485,045 - 44,558,870 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1644,485,049 - 44,558,897 (-)EnsemblGRCm38mm10GRCm38
MGSCv371644,485,158 - 44,558,983 (-)NCBIGRCm37mm9NCBIm37
MGSCv361644,404,377 - 44,478,202 (-)NCBImm8
Celera1644,843,888 - 44,917,724 (-)NCBICelera
Cytogenetic Map16B4NCBI
Boc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542713,424,478 - 13,493,952 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542713,424,478 - 13,492,527 (+)NCBIChiLan1.0ChiLan1.0
BOC
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13117,277,763 - 117,352,741 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3117,277,769 - 117,352,741 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03110,354,576 - 110,429,954 (+)NCBIMhudiblu_PPA_v0panPan3
BOC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3317,556,910 - 17,630,259 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13317,508,046 - 17,629,705 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Boc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936536813,984 - 890,766 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BOC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13146,625,957 - 146,703,936 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113146,625,218 - 146,703,165 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213156,163,631 - 156,182,841 (+)NCBISscrofa10.2Sscrofa10.2susScr3
BOC
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12267,552,105 - 67,635,557 (-)NCBI
ChlSab1.1 Ensembl2267,559,150 - 67,635,175 (-)Ensembl
Boc
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473135,256,658 - 35,330,274 (-)NCBI

Position Markers
BE110539  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01161,158,979 - 61,159,140NCBIRnor6.0
Rnor_5.01165,266,511 - 65,266,672UniSTSRnor5.0
RGSC_v3.41157,743,487 - 57,743,648UniSTSRGSC3.4
Celera1155,757,494 - 55,757,655UniSTS
RH 3.4 Map4623.62UniSTS
Cytogenetic Map11q21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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
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
1598811Bp291Blood pressure QTL 2911.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)112194422966944229Rat
1598841Memor7Memory QTL 7exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)112194422966944229Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112540112970401129Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112572003870720038Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112572003870720038Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112831466586994795Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)113043533963186373Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)113043533986714631Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113215552082443118Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113590063480900634Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114309033886714631Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)114444434769649708Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114658320986714631Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
4889859Pur28Proteinuria QTL 2819.50.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114790104978471527Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115785881090463843Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115994302390463843Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)116010984287141948Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:86
Count of miRNA genes:64
Interacting mature miRNAs:81
Transcripts:ENSRNOT00000002790
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
Medium 32 5 2 2 2 1 1 71 22 33 11 1
Low 3 11 36 23 17 23 7 10 3 13 8 7
Below cutoff 16 16 16

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002790   ⟹   ENSRNOP00000002790
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1161,083,757 - 61,158,838 (+)Ensembl
RefSeq Acc Id: NM_001108317   ⟹   NP_001101787
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21156,122,750 - 56,198,060 (+)NCBI
RefSeq Acc Id: XM_006221137   ⟹   XP_006221199
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1155,682,824 - 55,757,735 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006248353   ⟹   XP_006248415
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01161,084,216 - 61,159,220 (+)NCBI
Rnor_5.01165,191,723 - 65,266,748 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598157   ⟹   XP_017453646
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01161,120,139 - 61,159,220 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598158   ⟹   XP_017453647
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21156,122,697 - 56,198,056 (+)NCBI
Rnor_6.01161,120,139 - 61,159,220 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598159   ⟹   XP_017453648
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21156,122,697 - 56,198,056 (+)NCBI
Rnor_6.01161,120,139 - 61,159,220 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598160   ⟹   XP_017453649
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21156,122,697 - 56,198,056 (+)NCBI
Rnor_6.01161,120,139 - 61,159,220 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604349   ⟹   XP_017459838
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1155,718,749 - 55,757,735 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604350   ⟹   XP_017459839
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1155,718,749 - 55,757,735 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604351   ⟹   XP_017459840
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1155,718,749 - 55,757,735 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604352   ⟹   XP_017459841
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1155,718,749 - 55,757,735 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001101787 (Get FASTA)   NCBI Sequence Viewer  
  XP_017453647 (Get FASTA)   NCBI Sequence Viewer  
  XP_017453648 (Get FASTA)   NCBI Sequence Viewer  
  XP_017453649 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM11156 (Get FASTA)   NCBI Sequence Viewer  
  EDM11157 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_006221199   ⟸   XM_006221137
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006248415   ⟸   XM_006248353
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017459838   ⟸   XM_017604349
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017459839   ⟸   XM_017604350
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017459840   ⟸   XM_017604351
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017459841   ⟸   XM_017604352
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017453646   ⟸   XM_017598157
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017453647   ⟸   XM_017598158
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017453648   ⟸   XM_017598159
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017453649   ⟸   XM_017598160
- Peptide Label: isoform X3
- UniProtKB: D4A0Z7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002790   ⟸   ENSRNOT00000002790
RefSeq Acc Id: NP_001101787   ⟸   NM_001108317
- Peptide Label: precursor
Protein Domains
Fibronectin type-III   Ig-like

Transcriptome

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

Promoters
RGD ID:13698153
Promoter ID:EPDNEW_R8672
Type:single initiation site
Name:Boc_1
Description:BOC cell adhesion associated, oncogene regulated
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_6.01161,083,830 - 61,083,890EPDNEW

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)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 65264035 65264036 C T snv WKY/N (KNAW), GK/Ox (KNAW), WKY/NHsd (KNAW), WKY/NCrl (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 61156503 61156504 C T snv WKY/N (MCW), WKY/NHsd (RGD), WKY/NCrl (RGD), GK/Ox (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304550 AgrOrtholog
Ensembl Genes ENSRNOG00000002041 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002790 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002790 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro BOC UniProtKB/TrEMBL
  Fibronectin_type3 UniProtKB/TrEMBL
  FN3_sf 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
  Immunoglobulin UniProtKB/TrEMBL
NCBI Gene 360715 ENTREZGENE
PANTHER PTHR44170:SF3 UniProtKB/TrEMBL
Pfam fn3 UniProtKB/TrEMBL
  I-set UniProtKB/TrEMBL
  PF00047 UniProtKB/TrEMBL
PhenoGen Boc PhenoGen
PROSITE FN3 UniProtKB/TrEMBL
  IG_LIKE UniProtKB/TrEMBL
SMART FN3 UniProtKB/TrEMBL
  IGc2 UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP FN_III-like UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt D4A0Z7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-03-08 Boc  BOC cell adhesion associated, oncogene regulated  Boc  biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Boc  biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein   Boc_predicted  biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Boc_predicted  biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein (predicted)      Symbol and Name status set to approved 70820 APPROVED