Tmed11 (transmembrane emp24 protein transport domain containing 11) - Rat Genome Database

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Gene: Tmed11 (transmembrane emp24 protein transport domain containing 11) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Tmed11
Name: transmembrane emp24 protein transport domain containing 11
RGD ID: 1588776
Description: Predicted to enable cargo receptor activity. 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.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC689712; similar to Glycoprotein 25L precursor (GP25L); transmembrane emp24 domain-containing protein 11; transmembrane emp24 protein transport domain containing; transmembrane emp24 protein transport domain containing 4-like
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8141,071,410 - 1,091,793 (+)NCBIGRCr8
mRatBN7.214926,983 - 947,574 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl14927,001 - 947,321 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0141,936,972 - 1,959,089 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl141,937,041 - 1,957,579 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0141,932,659 - 1,953,450 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4141,466,847 - 1,487,827 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera14965,819 - 987,611 (+)NCBICelera
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Tmed11
94 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:13
Count of miRNA genes:13
Interacting mature miRNAs:13
Transcripts:ENSRNOT00000000040
Prediction methods:Miranda, Rnahybrid
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat

Markers in Region
D14Got1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214938,989 - 939,187 (+)MAPPERmRatBN7.2
mRatBN7.214938,989 - 939,366 (+)MAPPERmRatBN7.2
Rnor_6.0141,949,012 - 1,949,438NCBIRnor6.0
Rnor_6.0141,949,012 - 1,949,209NCBIRnor6.0
Rnor_5.0141,944,738 - 1,945,164UniSTSRnor5.0
Rnor_5.0141,944,738 - 1,944,935UniSTSRnor5.0
RGSC_v3.4141,479,488 - 1,479,686RGDRGSC3.4
RGSC_v3.4141,479,489 - 1,479,686UniSTSRGSC3.4
RGSC_v3.1141,479,488 - 1,479,686RGD
Celera14977,833 - 978,025UniSTS
RH 2.0 Map149.8RGD
Cytogenetic Map14p22UniSTS
AI178079  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214946,752 - 946,879 (+)MAPPERmRatBN7.2
Rnor_6.0141,957,011 - 1,957,137NCBIRnor6.0
Rnor_5.0141,952,737 - 1,952,863UniSTSRnor5.0
RGSC_v3.4141,487,259 - 1,487,385UniSTSRGSC3.4
Celera14985,533 - 985,659UniSTS
Cytogenetic Map14p22UniSTS


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
Low 5 5 8 5 1 10
Below cutoff 1 3 11 4 5 4 2 2 7 2 8 5 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000040   ⟹   ENSRNOP00000000040
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14927,001 - 947,321 (+)Ensembl
Rnor_6.0 Ensembl141,937,041 - 1,957,579 (+)Ensembl
RefSeq Acc Id: XM_001071744   ⟹   XP_001071744
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8141,071,410 - 1,091,793 (+)NCBI
mRatBN7.214926,983 - 947,574 (+)NCBI
Rnor_6.0141,936,972 - 1,959,089 (+)NCBI
Rnor_5.0141,932,659 - 1,953,450 (+)NCBI
RGSC_v3.4141,466,847 - 1,487,827 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs XP_001071744 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000000040
  ENSRNOP00000000040.1
Reference Protein Sequences
RefSeq Acc Id: XP_001071744   ⟸   XM_001071744
- UniProtKB: D3ZE21 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000040   ⟸   ENSRNOT00000000040
Protein Domains
GOLD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZE21-F1-model_v2 AlphaFold D3ZE21 1-214 view protein structure

Transcriptome

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

Promoters
RGD ID:13699158
Promoter ID:EPDNEW_R9666
Type:single initiation site
Name:Tmed11_1
Description:transmembrane emp24 protein transport domain containing 11
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_6.0141,936,986 - 1,937,046EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1588776 AgrOrtholog
BioCyc Gene G2FUF-16688 BioCyc
Ensembl Genes ENSRNOG00000000035 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000040.3 UniProtKB/TrEMBL
InterPro GOLD UniProtKB/TrEMBL
  TMP21-related UniProtKB/TrEMBL
KEGG Report rno:689712 UniProtKB/TrEMBL
NCBI Gene 689712 ENTREZGENE
PANTHER PTHR22811 UniProtKB/TrEMBL
  PTHR22811:SF3 UniProtKB/TrEMBL
Pfam EMP24_GP25L UniProtKB/TrEMBL
PhenoGen Tmed11 PhenoGen
PROSITE GOLD UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000035 RatGTEx
SMART EMP24_GP25L UniProtKB/TrEMBL
UniProt D3ZE21 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Tmed11  transmembrane emp24 protein transport domain containing 11  LOC100363761  transmembrane emp24 protein transport domain containing 4-like  Data merged from RGD:2322390 1643240 APPROVED
2012-02-03 Tmed11  transmembrane emp24 protein transport domain containing 11  Tmed11  transmembrane emp24 protein transport domain containing  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-06 LOC100363761  transmembrane emp24 protein transport domain containing 4-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-02-12 Tmed11  transmembrane emp24 protein transport domain containing  LOC689712  similar to Glycoprotein 25L precursor (GP25L)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC689712  similar to Glycoprotein 25L precursor (GP25L)  LOC682110  similar to Glycoprotein 25L precursor (GP25L)  Data merged from RGD:1586975 1643240 APPROVED
2006-11-19 LOC689712  similar to Glycoprotein 25L precursor (GP25L)      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC682110  similar to Glycoprotein 25L precursor (GP25L)      Symbol and Name status set to provisional 70820 PROVISIONAL