Tmed1 (transmembrane p24 trafficking protein 1) - Rat Genome Database

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Gene: Tmed1 (transmembrane p24 trafficking protein 1) Rattus norvegicus
Analyze
Symbol: Tmed1
Name: transmembrane p24 trafficking protein 1
RGD ID: 1311679
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; endoplasmic reticulum-Golgi intermediate compartment membrane; and plasma 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 TMED1 (transmembrane p24 trafficking protein 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Il1rl1l; interleukin 1 receptor-like 1 ligand; interleukin-1 receptor-like 1 ligand; LOC315461; MGC108769; p24 family protein gamma-1; p24gamma1; transmembrane emp24 domain containing 1; transmembrane emp24 domain-containing protein 1; transmembrane emp24 protein transport domain containing 1
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
GRCr8828,336,072 - 28,342,853 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl828,336,074 - 28,338,841 (-)EnsemblGRCr8
mRatBN7.2820,059,937 - 20,063,567 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl820,059,892 - 20,063,677 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx824,091,778 - 24,094,354 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0822,389,615 - 22,392,191 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0820,289,597 - 20,292,172 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0822,540,422 - 22,544,369 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl822,540,424 - 22,542,997 (-)Ensemblrn6Rnor6.0
Rnor_5.0822,594,533 - 22,598,482 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4820,611,139 - 20,613,714 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera821,451,162 - 21,453,737 (-)NCBICelera
RGSC_v3.1820,611,139 - 20,613,714 (-)NCBI
Cytogenetic Map8q13NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

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 GOA human gene data--August 2006 GOA data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:9472029   PMID:12237308   PMID:15489334  


Genomics

Comparative Map Data
Tmed1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8828,336,072 - 28,342,853 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl828,336,074 - 28,338,841 (-)EnsemblGRCr8
mRatBN7.2820,059,937 - 20,063,567 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl820,059,892 - 20,063,677 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx824,091,778 - 24,094,354 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0822,389,615 - 22,392,191 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0820,289,597 - 20,292,172 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0822,540,422 - 22,544,369 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl822,540,424 - 22,542,997 (-)Ensemblrn6Rnor6.0
Rnor_5.0822,594,533 - 22,598,482 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4820,611,139 - 20,613,714 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera821,451,162 - 21,453,737 (-)NCBICelera
RGSC_v3.1820,611,139 - 20,613,714 (-)NCBI
Cytogenetic Map8q13NCBI
TMED1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381910,832,067 - 10,836,212 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1910,832,067 - 10,836,318 (-)Ensemblhg38GRCh38
GRCh371910,942,743 - 10,946,888 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361910,804,114 - 10,807,983 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341910,804,114 - 10,807,983NCBI
Celera1910,837,959 - 10,841,828 (-)NCBICelera
Cytogenetic Map19p13.2NCBI
HuRef1910,520,875 - 10,525,115 (-)NCBIHuRef
CHM1_11910,943,980 - 10,948,220 (-)NCBICHM1_1
T2T-CHM13v2.01910,959,078 - 10,963,224 (-)NCBIT2T-CHM13v2.0
Tmed1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39921,418,676 - 21,421,530 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl921,418,849 - 21,421,548 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38921,507,380 - 21,510,234 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl921,507,553 - 21,510,252 (-)Ensemblmm10GRCm38
MGSCv37921,311,824 - 21,314,630 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36921,257,782 - 21,260,588 (-)NCBIMGSCv36mm8
Celera918,775,983 - 18,778,789 (-)NCBICelera
Cytogenetic Map9A3NCBI
cM Map97.81NCBI
Tmed1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554951,934,920 - 1,938,208 (-)Ensembl
ChiLan1.0NW_0049554951,934,920 - 1,938,208 (-)NCBIChiLan1.0ChiLan1.0
TMED1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22015,752,619 - 15,756,706 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11914,751,212 - 14,755,086 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01910,386,041 - 10,389,905 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11911,107,511 - 11,111,744 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1911,107,511 - 11,111,744 (-)EnsemblpanPan2panpan1.1
TMED1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12050,395,862 - 50,399,118 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2050,396,005 - 50,407,535 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2050,268,438 - 50,280,141 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02050,917,471 - 50,929,210 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2050,917,621 - 50,929,195 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12050,126,288 - 50,137,982 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02050,553,831 - 50,565,514 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02050,795,278 - 50,806,997 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tmed1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118209,305,083 - 209,308,562 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366591,042,139 - 1,049,628 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366591,046,144 - 1,049,628 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMED1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl269,568,354 - 69,576,066 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1269,573,128 - 69,576,421 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2270,006,707 - 70,009,745 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TMED1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.169,829,529 - 9,833,559 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl69,830,086 - 9,833,529 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366607410,119,327 - 10,123,764 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tmed1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248282,805,519 - 2,808,249 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248282,805,015 - 2,808,232 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Tmed1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1817,779,370 - 17,782,341 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tmed1
34 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:393
Count of miRNA genes:220
Interacting mature miRNAs:261
Transcripts:ENSRNOT00000061009
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)81699464261994642Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)81038254055382540Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)81296416557964165Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)81595227960952279Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)81296416557964165Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)81799386262252873Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)81038254055382540Rat
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8132882639Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)81038254055382540Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)81699464261994642Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)81296416557964165Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)81038254055382540Rat

Markers in Region
BE100267  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2820,062,581 - 20,062,750 (+)MAPPERmRatBN7.2
Rnor_6.0822,543,067 - 22,543,235NCBIRnor6.0
Rnor_5.0822,597,178 - 22,597,346UniSTSRnor5.0
RGSC_v3.4820,613,784 - 20,613,952UniSTSRGSC3.4
Celera821,453,807 - 21,453,975UniSTS
RH 3.4 Map8207.21UniSTS
Cytogenetic Map8q13UniSTS


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 12 67 165 91 90 59 91 59 6 355 191 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000061009   ⟹   ENSRNOP00000057728
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl828,336,074 - 28,338,659 (-)Ensembl
mRatBN7.2 Ensembl820,059,892 - 20,062,510 (-)Ensembl
Rnor_6.0 Ensembl822,540,424 - 22,542,997 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000100773   ⟹   ENSRNOP00000084813
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl828,336,074 - 28,338,841 (-)Ensembl
mRatBN7.2 Ensembl820,059,941 - 20,063,677 (-)Ensembl
RefSeq Acc Id: NM_001013432   ⟹   NP_001013450
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8828,336,072 - 28,338,647 (-)NCBI
mRatBN7.2820,059,937 - 20,062,512 (-)NCBI
Rnor_6.0822,540,422 - 22,542,997 (-)NCBI
Rnor_5.0822,594,533 - 22,598,482 (-)NCBI
RGSC_v3.4820,611,139 - 20,613,714 (-)RGD
Celera821,451,162 - 21,453,737 (-)RGD
Sequence:
RefSeq Acc Id: XM_006242644   ⟹   XP_006242706
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8828,336,072 - 28,342,853 (-)NCBI
mRatBN7.2820,059,937 - 20,063,567 (-)NCBI
Rnor_6.0822,540,422 - 22,544,369 (-)NCBI
Rnor_5.0822,594,533 - 22,598,482 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008765940   ⟹   XP_008764162
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8828,336,072 - 28,342,853 (-)NCBI
mRatBN7.2820,059,937 - 20,063,564 (-)NCBI
Rnor_6.0822,540,422 - 22,544,367 (-)NCBI
Sequence:
RefSeq Acc Id: NP_001013450   ⟸   NM_001013432
- Peptide Label: precursor
- UniProtKB: Q5BK85 (UniProtKB/Swiss-Prot),   A6JNS6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242706   ⟸   XM_006242644
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008764162   ⟸   XM_008765940
- Peptide Label: isoform X2
- UniProtKB: A0A8I6A1Y9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000057728   ⟸   ENSRNOT00000061009
Ensembl Acc Id: ENSRNOP00000084813   ⟸   ENSRNOT00000100773
Protein Domains
GOLD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5BK85-F1-model_v2 AlphaFold Q5BK85 1-227 view protein structure

Transcriptome

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

Promoters
RGD ID:13695781
Promoter ID:EPDNEW_R6306
Type:multiple initiation site
Name:Tmed1_1
Description:transmembrane p24 trafficking 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_6.0822,542,999 - 22,543,059EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311679 AgrOrtholog
BioCyc Gene G2FUF-31418 BioCyc
Ensembl Genes ENSRNOG00000008037 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000061009 ENTREZGENE
  ENSRNOT00000061009.5 UniProtKB/Swiss-Prot
  ENSRNOT00000100773 ENTREZGENE
IMAGE_CLONE IMAGE:7324543 IMAGE-MGC_LOAD
InterPro GOLD_dom UniProtKB/Swiss-Prot
  GOLD_dom_sf UniProtKB/Swiss-Prot
  TMP21-related UniProtKB/Swiss-Prot
KEGG Report rno:315461 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108769 IMAGE-MGC_LOAD
NCBI Gene 315461 ENTREZGENE
PANTHER PTHR22811 UniProtKB/Swiss-Prot
Pfam EMP24_GP25L UniProtKB/Swiss-Prot
PhenoGen Tmed1 PhenoGen
PROSITE GOLD UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000008037 RatGTEx
SMART EMP24_GP25L UniProtKB/Swiss-Prot
Superfamily-SCOP SSF101576 UniProtKB/Swiss-Prot
UniProt A0A8I6A1Y9 ENTREZGENE, UniProtKB/TrEMBL
  A6JNS6 ENTREZGENE, UniProtKB/TrEMBL
  Q5BK85 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-08-19 Tmed1  transmembrane p24 trafficking protein 1  Tmed1  transmembrane emp24 protein transport domain containing 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Tmed1  transmembrane emp24 protein transport domain containing 1  Tmed1  transmembrane emp24 domain containing 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-07-28 Tmed1  transmembrane emp24 domain containing 1  Il1rl1l  interleukin 1 receptor-like 1 ligand  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2005-12-06 Il1rl1l  interleukin 1 receptor-like 1 ligand  Il1rl1l_predicted  interleukin 1 receptor-like 1 ligand (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Il1rl1l_predicted  interleukin 1 receptor-like 1 ligand (predicted)      Symbol and Name status set to approved 70820 APPROVED