Tram1 (translocation associated membrane protein 1) - Rat Genome Database

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Gene: Tram1 (translocation associated membrane protein 1) Rattus norvegicus
Analyze
Symbol: Tram1
Name: translocation associated membrane protein 1
RGD ID: 1359100
Description: Predicted to be involved in SRP-dependent cotranslational protein targeting to membrane, translocation and protein insertion into ER membrane. Predicted to localize to integral component of endoplasmic reticulum membrane. Orthologous to human TRAM1 (translocation associated membrane protein 1); PARTICIPATES IN Endoplasmic Reticulum-associated degradation pathway; INTERACTS WITH 17beta-estradiol; 4,4'-diaminodiphenylmethane; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: MGC95042; translocating chain-associated membrane protein 1; translocating chain-associating membrane protein; translocating chain-associating membrane protein 1
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
NCBI Annotation Information: Note: There is an assembly problem in the Rnor_6.0 reference genome assembly, and therefore, annotation of this gene is split across NW_007905800.1 and NW_007905801.1 in NCBI's Rattus norvegicus Annotation Release 105. [18 Jun 2015]
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.255,642,579 - 5,667,666 (+)NCBI
Rnor_6.0 Ensembl55,215,196 - 5,316,685 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.055,215,196 - 5,297,337 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0510,062,171 - 10,062,451 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0510,121,579 - 10,138,210 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.454,844,208 - 4,869,207 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.154,844,207 - 4,869,206 (+)NCBI
Celera55,235,381 - 5,252,006 (+)NCBICelera
Cytogenetic Map5q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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:8698819   PMID:15489334   PMID:18555783   PMID:21237175   PMID:27105999   PMID:30338452  


Genomics

Comparative Map Data
Tram1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.255,642,579 - 5,667,666 (+)NCBI
Rnor_6.0 Ensembl55,215,196 - 5,316,685 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.055,215,196 - 5,297,337 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0510,062,171 - 10,062,451 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0510,121,579 - 10,138,210 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.454,844,208 - 4,869,207 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.154,844,207 - 4,869,206 (+)NCBI
Celera55,235,381 - 5,252,006 (+)NCBICelera
Cytogenetic Map5q11NCBI
TRAM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl870,573,218 - 70,608,416 (-)EnsemblGRCh38hg38GRCh38
GRCh38870,573,218 - 70,608,453 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37871,485,453 - 71,520,651 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36871,648,227 - 71,683,158 (-)NCBINCBI36hg18NCBI36
Build 34871,648,226 - 71,683,158NCBI
Celera867,483,078 - 67,518,322 (-)NCBI
Cytogenetic Map8q13.3NCBI
HuRef866,978,304 - 67,013,532 (-)NCBIHuRef
CHM1_1871,541,019 - 71,576,230 (-)NCBICHM1_1
Tram1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39113,634,917 - 13,660,134 (-)NCBIGRCm39mm39
GRCm39 Ensembl113,634,922 - 13,660,134 (-)Ensembl
GRCm38113,564,693 - 13,589,910 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl113,564,698 - 13,589,910 (-)EnsemblGRCm38mm10GRCm38
MGSCv37113,554,783 - 13,579,945 (-)NCBIGRCm37mm9NCBIm37
MGSCv36113,549,916 - 13,575,078 (-)NCBImm8
Celera113,514,581 - 13,539,714 (-)NCBICelera
Cytogenetic Map1A3NCBI
Tram1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554449,110,807 - 9,152,125 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554449,110,533 - 9,153,585 (+)NCBIChiLan1.0ChiLan1.0
TRAM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1868,759,038 - 68,793,750 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl868,759,040 - 68,794,303 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0867,098,588 - 67,133,511 (-)NCBIMhudiblu_PPA_v0panPan3
TRAM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12919,669,622 - 19,703,707 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2919,669,628 - 19,703,669 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2919,929,189 - 19,963,216 (-)NCBI
ROS_Cfam_1.02919,766,644 - 19,800,987 (-)NCBI
UMICH_Zoey_3.12919,804,740 - 19,838,512 (-)NCBI
UNSW_CanFamBas_1.02919,871,008 - 19,905,124 (-)NCBI
UU_Cfam_GSD_1.02920,151,950 - 20,186,017 (-)NCBI
Tram1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530359,528,340 - 59,551,780 (+)NCBI
SpeTri2.0NW_00493649615,233,692 - 15,257,085 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TRAM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl464,749,244 - 64,836,126 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1464,768,600 - 64,800,513 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2470,399,155 - 70,431,001 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TRAM1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1866,312,103 - 66,344,738 (-)NCBI
ChlSab1.1 Ensembl866,311,614 - 66,344,840 (-)Ensembl
Vero_WHO_p1.0NW_02366603975,081,633 - 75,114,264 (+)NCBI
Tram1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474420,618,963 - 20,653,285 (+)NCBI

Position Markers
RH134162  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.255,654,064 - 5,654,247 (+)MAPPER
Rnor_6.055,283,820 - 5,284,002NCBIRnor6.0
Rnor_5.0510,124,693 - 10,124,875UniSTSRnor5.0
RGSC_v3.454,855,690 - 4,855,872UniSTSRGSC3.4
Celera55,238,495 - 5,238,677UniSTS
RH 3.4 Map50.0UniSTS
Cytogenetic Map5q11UniSTS
RH136958  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.255,667,272 - 5,667,490 (+)MAPPER
Rnor_6.055,297,027 - 5,297,244NCBIRnor6.0
Rnor_5.0510,137,900 - 10,138,117UniSTSRnor5.0
RGSC_v3.454,868,897 - 4,869,114UniSTSRGSC3.4
Celera55,251,696 - 5,251,913UniSTS
Cytogenetic Map5q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5189432042Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5193273395Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51136640934Rat
2312562Pur18Proteinuria QTL 182.60.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5152509833001026Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5152509878720537Rat
631551Vetf1Vascular elastic tissue fragility QTL 150.0001aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)516665875533324Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5166658771552720Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5325132926252076Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5325132948722188Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5452573847978104Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:801
Count of miRNA genes:312
Interacting mature miRNAs:401
Transcripts:ENSRNOT00000010481, ENSRNOT00000045373
Prediction methods:Microtar, 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 3 43 57 41 19 41 6 8 74 35 41 11 6
Low 2 3 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000010481   ⟹   ENSRNOP00000010481
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl55,215,196 - 5,297,336 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000045373   ⟹   ENSRNOP00000045166
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl55,279,296 - 5,316,685 (+)Ensembl
RefSeq Acc Id: NM_001007701   ⟹   NP_001007702
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.255,642,624 - 5,667,583 (+)NCBI
Rnor_6.055,215,196 - 5,297,337 (+)NCBI
Rnor_5.0510,062,171 - 10,062,451 (+)NCBI
Rnor_5.0510,121,579 - 10,138,210 (+)NCBI
RGSC_v3.454,844,208 - 4,869,207 (+)RGD
Celera55,235,381 - 5,252,006 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039109743   ⟹   XP_038965671
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.255,642,579 - 5,667,666 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001007702 (Get FASTA)   NCBI Sequence Viewer  
  XP_038965671 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH83851 (Get FASTA)   NCBI Sequence Viewer  
  AAQ91025 (Get FASTA)   NCBI Sequence Viewer  
  Q5XI41 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001007702   ⟸   NM_001007701
- UniProtKB: Q5XI41 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000045166   ⟸   ENSRNOT00000045373
RefSeq Acc Id: ENSRNOP00000010481   ⟸   ENSRNOT00000010481
RefSeq Acc Id: XP_038965671   ⟸   XM_039109743
- Peptide Label: isoform X1
Protein Domains
TLC

Transcriptome

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

Promoters
RGD ID:13693531
Promoter ID:EPDNEW_R4055
Type:initiation region
Name:Tram1_1
Description:translocation associated membrane protein 1
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_6.055,215,246 - 5,215,306EPDNEW

Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359100 AgrOrtholog
Ensembl Genes ENSRNOG00000007892 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000010481 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000045166 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000010481 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000045373 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7123274 IMAGE-MGC_LOAD
InterPro TLC-dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRAM1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Translocation_assoc_membrane UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:312903 UniProtKB/Swiss-Prot
MGC_CLONE MGC:95042 IMAGE-MGC_LOAD
NCBI Gene 312903 ENTREZGENE
PANTHER PTHR12371 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam TRAM1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRAM_LAG1_CLN8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tram1 PhenoGen
PIRSF Translocation_assoc_membrane UniProtKB/Swiss-Prot
PROSITE TLC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART TLC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt Q5XI41 ENTREZGENE
  Q6TUH5_RAT UniProtKB/TrEMBL
  TRAM1_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-23 Tram1  translocation associated membrane protein 1  Tram1  translocating chain-associating membrane protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Tram1  translocating chain-associating membrane protein 1  Tram1  translocation associated membrane protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-11-17 Tram1  translocation associated membrane protein 1    translocating chain-associating membrane protein  Name updated 1299863 APPROVED
2005-07-29 Tram1  translocating chain-associating membrane protein      Symbol and Name status set to provisional 70820 PROVISIONAL