Tmem50b (transmembrane protein 50B) - Rat Genome Database
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Gene: Tmem50b (transmembrane protein 50B) Rattus norvegicus
Analyze
Symbol: Tmem50b
Name: transmembrane protein 50B
RGD ID: 1307561
Description: Predicted to be involved in late endosome to vacuole transport via multivesicular body sorting pathway. Predicted to localize to endoplasmic reticulum. Orthologous to human TMEM50B (transmembrane protein 50B); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; dibutyl phthalate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC360698; MGC109374; RGD1307561; similar to RIKEN cDNA B230114J08
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
mRatBN7.21130,804,835 - 30,837,675 (-)NCBI
Rnor_6.0 Ensembl1131,719,443 - 31,752,243 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01131,719,441 - 31,752,276 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01135,327,975 - 35,361,018 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41131,533,823 - 31,566,625 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11131,572,882 - 31,605,683 (-)NCBI
Celera1130,472,297 - 30,505,079 (-)NCBICelera
Cytogenetic Map11q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:16780588   PMID:18541381  


Genomics

Comparative Map Data
Tmem50b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21130,804,835 - 30,837,675 (-)NCBI
Rnor_6.0 Ensembl1131,719,443 - 31,752,243 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01131,719,441 - 31,752,276 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01135,327,975 - 35,361,018 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41131,533,823 - 31,566,625 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11131,572,882 - 31,605,683 (-)NCBI
Celera1130,472,297 - 30,505,079 (-)NCBICelera
Cytogenetic Map11q11NCBI
TMEM50B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2133,432,485 - 33,479,974 (-)EnsemblGRCh38hg38GRCh38
GRCh382133,432,486 - 33,480,004 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372134,804,793 - 34,852,281 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh372134,804,793 - 34,852,316 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362133,743,318 - 33,774,151 (-)NCBINCBI36hg18NCBI36
Build 342133,726,662 - 33,774,120NCBI
Celera2120,011,535 - 20,051,915 (-)NCBI
Cytogenetic Map21q22.11NCBI
HuRef2120,273,351 - 20,330,637 (-)NCBIHuRef
CHM1_12134,367,161 - 34,415,001 (-)NCBICHM1_1
Tmem50b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391691,371,390 - 91,394,568 (-)NCBIGRCm39mm39
GRCm381691,574,508 - 91,597,680 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1691,574,503 - 91,597,800 (-)EnsemblGRCm38mm10GRCm38
MGSCv371691,574,753 - 91,597,925 (-)NCBIGRCm37mm9NCBIm37
MGSCv361691,463,367 - 91,486,539 (-)NCBImm8
Celera1692,651,244 - 92,674,477 (-)NCBICelera
Cytogenetic Map16C3.3NCBI
Tmem50b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540732,874,905 - 32,916,036 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540732,876,380 - 32,916,036 (-)NCBIChiLan1.0ChiLan1.0
TMEM50B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12133,163,876 - 33,219,556 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2133,163,876 - 33,219,556 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02119,789,799 - 19,847,335 (-)NCBIMhudiblu_PPA_v0panPan3
TMEM50B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13128,061,730 - 28,117,485 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Tmem50b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365008,825,956 - 8,873,510 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMEM50B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13197,046,679 - 197,093,251 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113197,048,285 - 197,093,308 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
TMEM50B
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1258,701,542 - 58,730,311 (+)NCBI
ChlSab1.1 Ensembl258,701,557 - 58,733,139 (+)Ensembl
Tmem50b
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474521,649,759 - 21,704,734 (-)NCBI

Position Markers
D11Mco5  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01131,739,067 - 31,739,287NCBIRnor6.0
Rnor_6.01131,739,067 - 31,739,450NCBIRnor6.0
Rnor_5.01135,347,601 - 35,347,821UniSTSRnor5.0
Rnor_5.01135,347,601 - 35,347,984UniSTSRnor5.0
RGSC_v3.41131,553,448 - 31,553,669RGDRGSC3.4
RGSC_v3.41131,553,449 - 31,553,832UniSTSRGSC3.4
RGSC_v3.41131,553,449 - 31,553,669UniSTSRGSC3.4
RGSC_v3.11131,592,506 - 31,592,727RGD
Celera1130,491,905 - 30,492,122UniSTS
Celera1130,491,905 - 30,492,285UniSTS
Cytogenetic Map11q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11133867429Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11172720192Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)1132503169342559Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11935127454351274Rat
2290451Scl58Serum cholesterol level QTL 583.48blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)111136730644444347Rat
724517Uae18Urinary albumin excretion QTL 183.7urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)111632197346583360Rat
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
634341Bw121Body weight QTL 1213.56abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)112204314944444112Rat
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

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:716
Count of miRNA genes:289
Interacting mature miRNAs:363
Transcripts:ENSRNOT00000002775
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 15 1 17 1 8 11 74 35 39 11 8
Low 42 40 2 40 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002775   ⟹   ENSRNOP00000002775
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1131,719,443 - 31,752,243 (-)Ensembl
RefSeq Acc Id: NM_001025014   ⟹   NP_001020185
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,804,837 - 30,837,644 (-)NCBI
Rnor_6.01131,719,441 - 31,752,243 (-)NCBI
Rnor_5.01135,327,975 - 35,361,018 (-)NCBI
RGSC_v3.41131,533,823 - 31,566,625 (-)RGD
Celera1130,472,297 - 30,505,079 (-)RGD
Sequence:
RefSeq Acc Id: XM_006248066   ⟹   XP_006248128
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,804,835 - 30,837,674 (-)NCBI
Rnor_6.01131,719,441 - 31,752,276 (-)NCBI
Rnor_5.01135,327,975 - 35,361,018 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006248067   ⟹   XP_006248129
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,804,835 - 30,837,521 (-)NCBI
Rnor_6.01131,719,441 - 31,752,098 (-)NCBI
Rnor_5.01135,327,975 - 35,361,018 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006248068   ⟹   XP_006248130
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,804,835 - 30,837,521 (-)NCBI
Rnor_6.01131,719,441 - 31,752,098 (-)NCBI
Rnor_5.01135,327,975 - 35,361,018 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006248069   ⟹   XP_006248131
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01131,719,441 - 31,744,059 (-)NCBI
Rnor_5.01135,327,975 - 35,361,018 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598024   ⟹   XP_017453513
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,804,835 - 30,832,608 (-)NCBI
Rnor_6.01131,719,441 - 31,747,205 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598025   ⟹   XP_017453514
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,804,835 - 30,837,675 (-)NCBI
Rnor_6.01131,719,441 - 31,752,276 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039088458   ⟹   XP_038944386
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,804,835 - 30,837,661 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001020185   ⟸   NM_001025014
- UniProtKB: Q5BJS6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006248128   ⟸   XM_006248066
- Peptide Label: isoform X1
- UniProtKB: Q5BJS6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006248130   ⟸   XM_006248068
- Peptide Label: isoform X1
- UniProtKB: Q5BJS6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006248129   ⟸   XM_006248067
- Peptide Label: isoform X1
- UniProtKB: Q5BJS6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006248131   ⟸   XM_006248069
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017453514   ⟸   XM_017598025
- Peptide Label: isoform X1
- UniProtKB: Q5BJS6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017453513   ⟸   XM_017598024
- Peptide Label: isoform X1
- UniProtKB: Q5BJS6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002775   ⟸   ENSRNOT00000002775
RefSeq Acc Id: XP_038944386   ⟸   XM_039088458
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13698057
Promoter ID:EPDNEW_R8582
Type:initiation region
Name:Tmem50b_1
Description:transmembrane protein 50B
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_6.01131,752,240 - 31,752,300EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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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_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 31730212 31730213 A C snv SR/JrHsd (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307561 AgrOrtholog
Ensembl Genes ENSRNOG00000002028 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002775 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002775 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7316764 IMAGE-MGC_LOAD
InterPro UPF0220 UniProtKB/TrEMBL
KEGG Report rno:360698 UniProtKB/TrEMBL
MGC_CLONE MGC:109374 IMAGE-MGC_LOAD
NCBI Gene 360698 ENTREZGENE
PANTHER UPF0220 UniProtKB/TrEMBL
Pfam UPF0220 UniProtKB/TrEMBL
PhenoGen Tmem50b PhenoGen
UniProt Q5BJS6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Tmem50b  transmembrane protein 50B  RGD1307561  similar to RIKEN cDNA B230114J08  Symbol and Name updated 1299863 APPROVED
2005-12-06 RGD1307561  similar to RIKEN cDNA B230114J08  RGD1307561_predicted  similar to RIKEN cDNA B230114J08 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1307561_predicted  similar to RIKEN cDNA B230114J08 (predicted)  LOC360698_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC360698_predicted  similar to RIKEN cDNA B230114J08 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL