Gpm6b (glycoprotein m6b) - Rat Genome Database
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Gene: Gpm6b (glycoprotein m6b) Rattus norvegicus
Analyze
Symbol: Gpm6b
Name: glycoprotein m6b
RGD ID: 620580
Description: Predicted to be involved in several processes, including negative regulation of protein localization to cell surface; negative regulation of serotonin uptake; and positive regulation of bone mineralization. Predicted to localize to membrane raft and plasma membrane. Orthologous to human GPM6B (glycoprotein M6B); INTERACTS WITH 3,3',4,4',5-pentachlorobiphenyl; ammonium chloride; astemizole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: M6b; neuronal membrane glycoprotein M6-b; rhombencephalic expression protein-29 kDa; Rhombex-29
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
mRatBN7.2X28,057,788 - 28,204,409 (-)NCBI
Rnor_6.0 EnsemblX29,607,075 - 29,648,403 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X29,604,607 - 29,751,174 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X29,997,897 - 30,145,125 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X48,746,584 - 48,788,414 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X48,800,052 - 48,841,883 (-)NCBI
CeleraX28,432,966 - 28,474,260 (-)NCBICelera
Cytogenetic MapXq13-q14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6alpha-methylprednisolone  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
arsenous acid  (ISO)
astemizole  (EXP)
azathioprine  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bexarotene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butanal  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
cocaine  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
cyclosporin A  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
ethanol  (ISO)
etoposide  (ISO)
folic acid  (ISO)
furan  (EXP)
genistein  (ISO)
glycidol  (EXP)
indometacin  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
mercury dibromide  (ISO)
methapyrilene  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
miconazole  (ISO)
N-nitrosodiethylamine  (EXP)
nickel sulfate  (ISO)
oxaliplatin  (EXP)
p-chloromercuribenzoic acid  (ISO)
paracetamol  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
potassium chromate  (ISO)
prednisolone  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium aurothiomalate  (ISO)
sulforaphane  (ISO)
testosterone enanthate  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
xylitol  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:18581270   PMID:21638316   PMID:22871113   PMID:29282769  


Genomics

Comparative Map Data
Gpm6b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X28,057,788 - 28,204,409 (-)NCBI
Rnor_6.0 EnsemblX29,607,075 - 29,648,403 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X29,604,607 - 29,751,174 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X29,997,897 - 30,145,125 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X48,746,584 - 48,788,414 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X48,800,052 - 48,841,883 (-)NCBI
CeleraX28,432,966 - 28,474,260 (-)NCBICelera
Cytogenetic MapXq13-q14NCBI
GPM6B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX13,770,939 - 13,938,638 (-)EnsemblGRCh38hg38GRCh38
GRCh38X13,770,922 - 13,938,713 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X13,789,058 - 13,956,757 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X13,698,983 - 13,866,752 (-)NCBINCBI36hg18NCBI36
Build 34X13,551,753 - 13,594,971NCBI
CeleraX17,906,144 - 18,072,735 (-)NCBI
Cytogenetic MapXp22.2NCBI
HuRefX11,546,522 - 11,713,553 (-)NCBIHuRef
CHM1_1X13,819,859 - 13,987,377 (-)NCBICHM1_1
Gpm6b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X165,021,775 - 165,172,029 (+)NCBIGRCm39mm39
GRCm39 EnsemblX165,021,907 - 165,171,984 (+)Ensembl
GRCm38X166,238,943 - 166,389,033 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX166,238,911 - 166,388,988 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X162,676,875 - 162,826,965 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X161,583,077 - 161,733,093 (+)NCBImm8
CeleraX149,417,598 - 149,568,704 (+)NCBICelera
Cytogenetic MapXF5NCBI
Gpm6b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555194,287,026 - 4,432,188 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555194,287,203 - 4,432,188 (+)NCBIChiLan1.0ChiLan1.0
GPM6B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X13,666,106 - 13,711,964 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX13,666,192 - 13,711,964 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X6,377,913 - 6,544,826 (-)NCBIMhudiblu_PPA_v0panPan3
GPM6B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 EnsemblX10,214,933 - 10,374,837 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1X10,214,889 - 10,375,151 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Gpm6b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364703,332,856 - 3,496,178 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GPM6B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX10,430,281 - 10,643,429 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X10,429,496 - 10,582,768 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X11,383,146 - 11,536,257 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GPM6B
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X12,258,386 - 12,429,883 (-)NCBI
Gpm6b
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624882220,267 - 374,912 (+)NCBI

Position Markers
DXRat108  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X29,642,179 - 29,642,357NCBIRnor6.0
Rnor_5.0X30,035,541 - 30,035,719UniSTSRnor5.0
RGSC_v3.4X48,782,190 - 48,782,368UniSTSRGSC3.4
RGSC_v3.4X48,782,189 - 48,782,368RGDRGSC3.4
RGSC_v3.1X48,835,659 - 48,835,837RGD
CeleraX28,468,036 - 28,468,214UniSTS
RH 3.4 MapX375.1RGD
RH 3.4 MapX375.1UniSTS
RH 2.0 Map21293.4RGD
FHH x ACI MapX12.36RGD
Cytogenetic MapXq21UniSTS
RH133686  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X29,607,284 - 29,607,485NCBIRnor6.0
Rnor_5.0X30,000,574 - 30,000,775UniSTSRnor5.0
RGSC_v3.4X48,746,793 - 48,746,994UniSTSRGSC3.4
CeleraX28,433,175 - 28,433,376UniSTS
RH 3.4 MapX360.2UniSTS
Cytogenetic MapXq21UniSTS
RH138360  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X29,611,763 - 29,611,882NCBIRnor6.0
Rnor_5.0X30,005,053 - 30,005,172UniSTSRnor5.0
RGSC_v3.4X48,751,272 - 48,751,391UniSTSRGSC3.4
CeleraX28,437,654 - 28,437,773UniSTS
RH 3.4 MapX362.0UniSTS
Cytogenetic MapXq21UniSTS
GPM6B  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X29,621,329 - 29,621,494NCBIRnor6.0
Rnor_5.0X30,014,619 - 30,014,784UniSTSRnor5.0
RGSC_v3.4X48,760,838 - 48,761,003UniSTSRGSC3.4
CeleraX28,447,224 - 28,447,389UniSTS
Cytogenetic MapXq21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X144092703Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X166260933443848Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X428214049282140Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X595407850954078Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1815335263153352Rat
1598873Memor2Memory QTL 22.5exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)X2159262344320739Rat
2290375Gluco34Glucose level QTL 342.75blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X2159262344468300Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:547
Count of miRNA genes:258
Interacting mature miRNAs:325
Transcripts:ENSRNOT00000006777
Prediction methods:Microtar, Miranda, Pita, 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 18 11 4 4 74 22 32 11 4
Low 3 25 56 40 8 40 4 7 13 9 4
Below cutoff 1 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_138846 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256849 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256850 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256851 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773151 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601904 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099441 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099442 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB036421 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC112090 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC130009 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474014 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211882 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212903 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216347 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000383 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000006777   ⟹   ENSRNOP00000006777
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX29,607,075 - 29,648,403 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086721   ⟹   ENSRNOP00000070988
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX29,609,377 - 29,648,359 (-)Ensembl
RefSeq Acc Id: NM_138846   ⟹   NP_620201
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X28,060,256 - 28,101,588 (-)NCBI
Rnor_6.0X29,607,075 - 29,648,403 (-)NCBI
Rnor_5.0X29,997,897 - 30,145,125 (-)NCBI
RGSC_v3.4X48,746,584 - 48,788,414 (-)RGD
CeleraX28,432,966 - 28,474,260 (-)RGD
Sequence:
RefSeq Acc Id: XM_006256849   ⟹   XP_006256911
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X28,057,788 - 28,101,742 (-)NCBI
Rnor_6.0X29,604,607 - 29,648,557 (-)NCBI
Rnor_5.0X29,997,897 - 30,145,125 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256850   ⟹   XP_006256912
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X28,057,788 - 28,101,742 (-)NCBI
Rnor_6.0X29,606,624 - 29,648,557 (-)NCBI
Rnor_5.0X29,997,897 - 30,145,125 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256851   ⟹   XP_006256913
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X28,057,788 - 28,101,622 (-)NCBI
Rnor_6.0X29,604,607 - 29,648,512 (-)NCBI
Rnor_5.0X29,997,897 - 30,145,125 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773151   ⟹   XP_008771373
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X28,057,788 - 28,204,142 (-)NCBI
Rnor_6.0X29,604,607 - 29,750,943 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601904   ⟹   XP_017457393
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X28,057,788 - 28,204,409 (-)NCBI
Rnor_6.0X29,604,607 - 29,751,174 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099441   ⟹   XP_038955369
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X28,057,788 - 28,097,603 (-)NCBI
RefSeq Acc Id: XM_039099442   ⟹   XP_038955370
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X28,062,569 - 28,101,742 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_620201   ⟸   NM_138846
- Sequence:
RefSeq Acc Id: XP_006256911   ⟸   XM_006256849
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006256913   ⟸   XM_006256851
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006256912   ⟸   XM_006256850
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008771373   ⟸   XM_008773151
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017457393   ⟸   XM_017601904
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: ENSRNOP00000006777   ⟸   ENSRNOT00000006777
RefSeq Acc Id: ENSRNOP00000070988   ⟸   ENSRNOT00000086721
RefSeq Acc Id: XP_038955369   ⟸   XM_039099441
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038955370   ⟸   XM_039099442
- Peptide Label: isoform X4

Transcriptome

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

Promoters
RGD ID:13701797
Promoter ID:EPDNEW_R12314
Type:initiation region
Name:Gpm6b_1
Description:glycoprotein m6b
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_6.0X29,648,350 - 29,648,410EPDNEW

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:620580 AgrOrtholog
Ensembl Genes ENSRNOG00000004613 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000006777 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070988 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006777 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000086721 UniProtKB/TrEMBL
InterPro Myelin_PLP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Myelin_PLP_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:192179 UniProtKB/Swiss-Prot
NCBI Gene 192179 ENTREZGENE
PANTHER PTHR11683 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Myelin_PLP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Gpm6b PhenoGen
PRINTS MYELINPLP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE MYELIN_PLP_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MYELIN_PLP_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART PLP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JZB8_RAT UniProtKB/TrEMBL
  E9PSV8_RAT UniProtKB/TrEMBL
  GPM6B_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Gpm6b  glycoprotein m6b      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Gpm6b  glycoprotein m6b      Symbol and Name status set to provisional 70820 PROVISIONAL