Mouse Gene Tmed7 (uc008evr.2) Description and Page Index
  Description: transmembrane emp24 protein transport domain
Transcript (Including UTRs)
   Position: mm9 chr18:46,745,582-46,757,189 Size: 11,608 Total Exon Count: 3 Strand: -
Coding Region
   Position: mm9 chr18:46,748,106-46,756,936 Size: 8,831 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsCTDMicroarray ExpressionRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated: 2011-03-02

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr18:46,745,582-46,757,189)mRNA (may differ from genome)Protein (224 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAllen Brain Atlas
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
MGIPubMedReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: D3YZZ5_MOUSE
DESCRIPTION: SubName: Full=Protein Tmed7;
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein (By similarity).
SIMILARITY: Belongs to the EMP24/GP25L family.
SIMILARITY: Contains 1 GOLD domain.
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  Microarray Expression Data
 
Expression ratio colors:

GNF Expression Atlas 2 Data from GNF1M Mouse Chip

    
     
      
       
     
    
   
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Rinn et. al Sex Gene Expression Data on MOE430A Chip

        
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GNF Expression Atlas Data from U74a Mouse Chip

        
     
    
    
    
   
    
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -122.80253-0.485 Picture PostScript Text
3' UTR -613.732524-0.243 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR009038 - GOLD
IPR015718 - P24-related

Pfam Domains:
PF01105 - emp24/gp25L/p24 family/GOLD

SCOP Domains:
101576 - Supernatant protein factor (SPF), C-terminal domain

ModBase Predicted Comparative 3D Structure on D3YZZ5
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserNo orthologGenome BrowserNo orthologGenome BrowserNo ortholog
Gene Details   Gene Details 
Gene Sorter   Gene Sorter 
GenBank Ensembl WormBase 
Protein Sequence Protein Sequence Protein Sequence 
Alignment Alignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function

Biological Process:
GO:0008150 biological_process

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005793 endoplasmic reticulum-Golgi intermediate compartment
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK077807 - Mus musculus adult male thymus cDNA, RIKEN full-length enriched library, clone:5830493P14 product:unclassifiable, full insert sequence.
AK147412 - Mus musculus cDNA, RIKEN full-length enriched library, clone:M5C1034P18 product:unclassifiable, full insert sequence.
BC024647 - Mus musculus transmembrane emp24 protein transport domain containing 7, mRNA (cDNA clone IMAGE:3985067).
BC018585 - Mus musculus transmembrane emp24 protein transport domain containing 7, mRNA (cDNA clone IMAGE:3986592).
AK076210 - Mus musculus 13 days embryo whole body cDNA, RIKEN full-length enriched library, clone:3930401E15 product:similar to P24B PROTEIN PRECURSOR (INTEGRAL TYPE I PROTEIN) (SIMILAR TO INTEGRAL TYPE I PROTEIN) [Homo sapiens], full insert sequence.
AK013936 - Mus musculus 13 days embryo head cDNA, RIKEN full-length enriched library, clone:3110001B13 product:weakly similar to P24B PROTEIN PRECURSOR (INTEGRAL TYPE I PROTEIN) (SIMILAR TO INTEGRAL TYPE I PROTEIN) [Homo sapiens], full insert sequence.
AK200376 - Mus musculus cDNA, clone:Y1G0134F24, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000036030, based on BLAT search.
AK029576 - Mus musculus adult male testis cDNA, RIKEN full-length enriched library, clone:4930402I03 product:weakly similar to CDNA FLJ14606 FIS, CLONE NT2RP1000547, WEAKLY SIMILAR TO COP-COATED VESICLE MEMBRANE PROTEIN P24 PRECURSOR [Homo sapiens], full insert sequence.
AK202734 - Mus musculus cDNA, clone:Y1G0142I17, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000036030, based on BLAT search.
AK180182 - Mus musculus cDNA, clone:Y0G0113D13, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000036030, based on BLAT search.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein D3YZZ5 (Reactome details) participates in the following event(s):

R-MMU-6807875 ARFGAP, cargo, v-SNAREs and p24 proteins bind nascent COPI complex
R-MMU-6811417 ARFGAP, cargo, vSNARES and p24 proteins bind COPI vesicles at Golgi
R-MMU-6807877 ARFGAPs stimulate ARF GTPase activity
R-MMU-6809003 ERGIC-to-Golgi vesicles bind dynein:dynactin
R-MMU-6811426 Retrograde COPI vesicles bind kinesin and microtubules
R-MMU-6811418 ARFGAPs stimulate ARF GTPase activity at the Golgi membrane
R-MMU-6811423 Retrograde vesicle is tethered at the ER by the NRZ complex and t-SNAREs
R-MMU-6809006 Vesicle is tethered through binding GOLGA2:GORASP1, GOLGB1 and the COG complex
R-MMU-6809011 cis-Golgi t-SNAREs bind YKT6 on tethered vesicle
R-MMU-6807878 COPI-mediated anterograde transport
R-MMU-6811434 COPI-dependent Golgi-to-ER retrograde traffic
R-MMU-199977 ER to Golgi Anterograde Transport
R-MMU-8856688 Golgi-to-ER retrograde transport
R-MMU-199991 Membrane Trafficking
R-MMU-948021 Transport to the Golgi and subsequent modification
R-MMU-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-MMU-5653656 Vesicle-mediated transport
R-MMU-446203 Asparagine N-linked glycosylation
R-MMU-597592 Post-translational protein modification
R-MMU-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: D3YZZ5, D3YZZ5_MOUSE, NM_025698, NP_079974, uc008evr.1
UCSC ID: uc008evr.2
RefSeq Accession: NM_025698
Protein: D3YZZ5 CCDS: CCDS50283.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_025698.1
exon count: 3CDS single in 3' UTR: no RNA size: 3452
ORF size: 675CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1550.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.