Tmed6 (transmembrane p24 trafficking protein 6) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Tmed6 (transmembrane p24 trafficking protein 6) Rattus norvegicus
Analyze
Symbol: Tmed6
Name: transmembrane p24 trafficking protein 6
RGD ID: 1305260
Description: Predicted to be involved in Golgi organization; endoplasmic reticulum to Golgi vesicle-mediated transport; and intracellular protein transport. Predicted to be located in endoplasmic reticulum membrane. Predicted to be active in several cellular components, including COPII-coated ER to Golgi transport vesicle; Golgi apparatus; and endoplasmic reticulum-Golgi intermediate compartment. Orthologous to human TMED6 (transmembrane p24 trafficking protein 6); INTERACTS WITH amitrole; bisphenol A; dibutyl phthalate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC291991; RGD1305260; similar to RIKEN cDNA 1810015P03; transmembrane emp24 domain-containing protein 6; transmembrane emp24 protein transport domain containing 6
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81951,876,561 - 51,882,648 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1951,876,561 - 51,882,648 (-)EnsemblGRCr8
mRatBN7.21934,966,813 - 34,972,900 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1934,966,813 - 34,972,900 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1941,782,291 - 41,788,378 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01942,435,638 - 42,441,725 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01944,734,666 - 44,740,770 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01939,261,841 - 39,267,928 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1939,261,841 - 39,267,928 (-)Ensemblrn6Rnor6.0
Rnor_5.01950,125,752 - 50,132,047 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41936,919,407 - 36,925,919 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1934,390,446 - 34,396,533 (-)NCBICelera
RGSC_v3.11936,924,402 - 36,930,795 (-)NCBI
Cytogenetic Map19q12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:22129529  


Genomics

Comparative Map Data
Tmed6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81951,876,561 - 51,882,648 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1951,876,561 - 51,882,648 (-)EnsemblGRCr8
mRatBN7.21934,966,813 - 34,972,900 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1934,966,813 - 34,972,900 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1941,782,291 - 41,788,378 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01942,435,638 - 42,441,725 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01944,734,666 - 44,740,770 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01939,261,841 - 39,267,928 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1939,261,841 - 39,267,928 (-)Ensemblrn6Rnor6.0
Rnor_5.01950,125,752 - 50,132,047 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41936,919,407 - 36,925,919 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1934,390,446 - 34,396,533 (-)NCBICelera
RGSC_v3.11936,924,402 - 36,930,795 (-)NCBI
Cytogenetic Map19q12NCBI
TMED6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381669,343,250 - 69,351,786 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1669,343,250 - 69,351,786 (-)Ensemblhg38GRCh38
GRCh371669,377,153 - 69,385,689 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361667,934,661 - 67,943,190 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341667,934,660 - 67,943,190NCBI
Celera1653,891,689 - 53,900,252 (-)NCBICelera
Cytogenetic Map16q22.1NCBI
HuRef1655,254,923 - 55,263,485 (-)NCBIHuRef
CHM1_11670,785,165 - 70,793,728 (-)NCBICHM1_1
T2T-CHM13v2.01675,144,944 - 75,153,477 (-)NCBIT2T-CHM13v2.0
Tmed6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398107,788,116 - 107,792,276 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8107,788,108 - 107,792,276 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm388107,061,484 - 107,065,644 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8107,061,476 - 107,065,644 (-)Ensemblmm10GRCm38
MGSCv378109,585,384 - 109,589,544 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv368109,950,613 - 109,954,773 (-)NCBIMGSCv36mm8
Celera8111,288,213 - 111,292,349 (-)NCBICelera
Cytogenetic Map8D3NCBI
cM Map853.58NCBI
Tmed6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554847,346,942 - 7,354,695 (+)Ensembl
ChiLan1.0NW_0049554847,346,942 - 7,354,695 (+)NCBIChiLan1.0ChiLan1.0
TMED6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21878,887,717 - 78,896,377 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11684,799,336 - 84,811,529 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01649,717,583 - 49,726,836 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11669,103,720 - 69,112,535 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1669,103,720 - 69,112,535 (-)EnsemblpanPan2panpan1.1
TMED6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1580,305,804 - 80,313,307 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha580,296,746 - 80,303,634 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0580,740,345 - 80,747,244 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl580,741,125 - 80,747,027 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1580,567,491 - 80,574,373 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0580,250,325 - 80,257,215 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0580,889,920 - 80,896,810 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tmed6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934940,119,751 - 40,129,270 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647519,459,883 - 19,467,368 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493647519,459,873 - 19,468,747 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMED6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl617,634,366 - 17,641,903 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1617,633,653 - 17,641,915 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2616,580,399 - 16,588,628 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TMED6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1558,054,903 - 58,063,685 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl558,055,595 - 58,062,917 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604720,784,894 - 20,793,480 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tmed6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474617,023,955 - 17,031,619 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462474617,024,204 - 17,031,358 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Tmed6
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11726,788,286 - 26,794,336 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tmed6
88 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:22
Count of miRNA genes:20
Interacting mature miRNAs:22
Transcripts:ENSRNOT00000027686
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19799775052997750Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)191922068964220689Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19799775052997750Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032907674246245Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)194622677874246245Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)193236531174246245Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)192409397369093973Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191083361874246245Rat
2303628Vencon9Ventilatory control QTL 90.005respiration trait (VT:0001943)minute ventilation (CMO:0000132)192318858668188586Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)194438513474246245Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)193253961574246245Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19799775052997750Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19799775052997750Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)193177788874246245Rat
1554318Bmd5Bone mineral density QTL 512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)192318858668188586Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)192010930665109306Rat
1354607Gmadr1Adrenal mass QTL 15.83adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)194072709254856850Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
1354600Salc2Saline consumption QTL 29.910.001drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)194072709254856850Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)194172254674246245Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat
1354633Bw28Body weight QTL 286.04body mass (VT:0001259)body weight (CMO:0000012)194072709254856850Rat

Markers in Region
RH131423  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21934,966,815 - 34,966,967 (+)MAPPERmRatBN7.2
Rnor_6.01939,261,844 - 39,261,995NCBIRnor6.0
Rnor_5.01950,125,755 - 50,125,906UniSTSRnor5.0
RGSC_v3.41936,919,410 - 36,919,561UniSTSRGSC3.4
Celera1934,390,449 - 34,390,600UniSTS
RH 3.4 Map19314.6UniSTS
Cytogenetic Map19q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 8 10 42 65 66 37 53 37 3 214 77 1 29 79 86 29 4 4

Sequence


Ensembl Acc Id: ENSRNOT00000027686   ⟹   ENSRNOP00000027686
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1951,876,561 - 51,882,648 (-)Ensembl
mRatBN7.2 Ensembl1934,966,813 - 34,972,900 (-)Ensembl
Rnor_6.0 Ensembl1939,261,841 - 39,267,928 (-)Ensembl
RefSeq Acc Id: NM_001106183   ⟹   NP_001099653
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81951,876,561 - 51,882,648 (-)NCBI
mRatBN7.21934,966,813 - 34,972,900 (-)NCBI
Rnor_6.01939,261,841 - 39,267,928 (-)NCBI
Rnor_5.01950,125,752 - 50,132,047 (-)NCBI
RGSC_v3.41936,919,407 - 36,925,919 (-)RGD
Celera1934,390,446 - 34,396,533 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001099653 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92469 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000027686
  ENSRNOP00000027686.4
RefSeq Acc Id: NP_001099653   ⟸   NM_001106183
- Peptide Label: precursor
- UniProtKB: D3ZJV9 (UniProtKB/TrEMBL),   A6IYZ1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000027686   ⟸   ENSRNOT00000027686
Protein Domains
GOLD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZJV9-F1-model_v2 AlphaFold D3ZJV9 1-238 view protein structure

Transcriptome

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

Promoters
RGD ID:13701121
Promoter ID:EPDNEW_R11645
Type:multiple initiation site
Name:Tmed6_1
Description:transmembrane p24 trafficking protein 6
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_6.01939,267,921 - 39,267,981EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305260 AgrOrtholog
BioCyc Gene G2FUF-5764 BioCyc
Ensembl Genes ENSRNOG00000020406 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027686 ENTREZGENE
  ENSRNOT00000027686.7 UniProtKB/TrEMBL
InterPro GOLD UniProtKB/TrEMBL
  TMP21-related UniProtKB/TrEMBL
KEGG Report rno:291991 UniProtKB/TrEMBL
NCBI Gene 291991 ENTREZGENE
PANTHER PTHR22811 UniProtKB/TrEMBL
Pfam EMP24_GP25L UniProtKB/TrEMBL
PhenoGen Tmed6 PhenoGen
PROSITE GOLD UniProtKB/TrEMBL
RatGTEx ENSRNOG00000020406 RatGTEx
SMART EMP24_GP25L UniProtKB/TrEMBL
UniProt A6IYZ1 ENTREZGENE, UniProtKB/TrEMBL
  D3ZJV9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-08-19 Tmed6  transmembrane p24 trafficking protein 6  Tmed6  transmembrane emp24 protein transport domain containing 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Tmed6  transmembrane emp24 protein transport domain containing 6   Tmed6_predicted  transmembrane emp24 protein transport domain containing 6 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Tmed6_predicted  transmembrane emp24 protein transport domain containing 6 (predicted)  RGD1305260_predicted  similar to RIKEN cDNA 1810015P03 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1305260_predicted  similar to RIKEN cDNA 1810015P03 (predicted)  LOC291991_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC291991_predicted  similar to RIKEN cDNA 1810015P03 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL