Human Gene TRARG1 (uc002fsi.1)
  Description: Homo sapiens tumor suppressor candidate 5 (TRARG1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr17:1,182,957-1,204,281 Size: 21,325 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr17:1,183,296-1,201,558 Size: 18,263 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:1,182,957-1,204,281)mRNA (may differ from genome)Protein (177 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHPRDLynxMGIneXtProtOMIM
PubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TUSC5_HUMAN
DESCRIPTION: RecName: Full=Tumor suppressor candidate 5; AltName: Full=Dispanin subfamily B member 1; Short=DSPB1; AltName: Full=Interferon-induced transmembrane domain-containing protein D3; AltName: Full=Protein located at seventeen-p-thirteen point three 1;
FUNCTION: May be involved in fat metabolism (By similarity).
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (Potential).
TISSUE SPECIFICITY: Expressed at high levels in heart, mammary gland, adrenal gland, stomach, smooth muscle and skeletal muscle, and at lower levels in brain and lung. Strongly down-regulated in lung cancer tissues, due to hypermethylation of the corresponding locus.
DEVELOPMENTAL STAGE: Expressed in fetal brain.
SIMILARITY: Belongs to the CD225/Dispanin family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 65.63 RPKM in Adipose - Visceral (Omentum)
Total median expression: 197.02 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -135.19339-0.399 Picture PostScript Text
3' UTR -1217.472723-0.447 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
IPR007593 - Interferon-induced_TM_protein

Pfam Domains:
PF04505 - Interferon-induced transmembrane protein

ModBase Predicted Comparative 3D Structure on Q8IXB3
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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0009607 response to biotic stimulus
GO:0032869 cellular response to insulin stimulus
GO:0044381 glucose import in response to insulin stimulus
GO:0045026 plasma membrane fusion
GO:0072659 protein localization to plasma membrane
GO:0099638 endosome to plasma membrane protein transport

Cellular Component:
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030659 cytoplasmic vesicle membrane


-  Descriptions from all associated GenBank mRNAs
  AB090231 - Homo sapiens mRNA for LOST1, complete cds.
BC142615 - Homo sapiens tumor suppressor candidate 5, mRNA (cDNA clone MGC:164777 IMAGE:40147346), complete cds.
JD541424 - Sequence 522448 from Patent EP1572962.
JD360715 - Sequence 341739 from Patent EP1572962.
JD485477 - Sequence 466501 from Patent EP1572962.
JD452972 - Sequence 433996 from Patent EP1572962.
JD453011 - Sequence 434035 from Patent EP1572962.
JD193338 - Sequence 174362 from Patent EP1572962.
JD335084 - Sequence 316108 from Patent EP1572962.
JD554112 - Sequence 535136 from Patent EP1572962.
JD382967 - Sequence 363991 from Patent EP1572962.
JD365431 - Sequence 346455 from Patent EP1572962.
JD191041 - Sequence 172065 from Patent EP1572962.
AB587551 - Synthetic construct DNA, clone: pF1KE1069, Homo sapiens TUSC5 gene for tumor suppressor candidate 5, without stop codon, in Flexi system.
KJ904176 - Synthetic construct Homo sapiens clone ccsbBroadEn_13570 TUSC5 gene, encodes complete protein.
AL831929 - Homo sapiens mRNA; cDNA DKFZp667O0510 (from clone DKFZp667O0510).
JD326364 - Sequence 307388 from Patent EP1572962.
JD217886 - Sequence 198910 from Patent EP1572962.
JD099169 - Sequence 80193 from Patent EP1572962.
JD209584 - Sequence 190608 from Patent EP1572962.
JD373768 - Sequence 354792 from Patent EP1572962.
JD252918 - Sequence 233942 from Patent EP1572962.
JD375060 - Sequence 356084 from Patent EP1572962.
JD531186 - Sequence 512210 from Patent EP1572962.
JD121252 - Sequence 102276 from Patent EP1572962.
JD186343 - Sequence 167367 from Patent EP1572962.
JD221676 - Sequence 202700 from Patent EP1572962.
JD391670 - Sequence 372694 from Patent EP1572962.
JD461114 - Sequence 442138 from Patent EP1572962.
JD450368 - Sequence 431392 from Patent EP1572962.
JD128393 - Sequence 109417 from Patent EP1572962.
JD207433 - Sequence 188457 from Patent EP1572962.
JD183037 - Sequence 164061 from Patent EP1572962.
JD130509 - Sequence 111533 from Patent EP1572962.
JD160137 - Sequence 141161 from Patent EP1572962.
JD470347 - Sequence 451371 from Patent EP1572962.
JD218840 - Sequence 199864 from Patent EP1572962.
JD429568 - Sequence 410592 from Patent EP1572962.
JD144469 - Sequence 125493 from Patent EP1572962.
JD231439 - Sequence 212463 from Patent EP1572962.
JD121814 - Sequence 102838 from Patent EP1572962.
JD321495 - Sequence 302519 from Patent EP1572962.
JD432801 - Sequence 413825 from Patent EP1572962.
JD514791 - Sequence 495815 from Patent EP1572962.
JD055584 - Sequence 36608 from Patent EP1572962.
JD055566 - Sequence 36590 from Patent EP1572962.
JD248297 - Sequence 229321 from Patent EP1572962.
JD075760 - Sequence 56784 from Patent EP1572962.
JD125914 - Sequence 106938 from Patent EP1572962.
JD565275 - Sequence 546299 from Patent EP1572962.
JD057605 - Sequence 38629 from Patent EP1572962.
JD076233 - Sequence 57257 from Patent EP1572962.
JD060507 - Sequence 41531 from Patent EP1572962.
JD152671 - Sequence 133695 from Patent EP1572962.
JD079040 - Sequence 60064 from Patent EP1572962.
JD289841 - Sequence 270865 from Patent EP1572962.
JD097144 - Sequence 78168 from Patent EP1572962.
JD156109 - Sequence 137133 from Patent EP1572962.
JD340243 - Sequence 321267 from Patent EP1572962.
JD462296 - Sequence 443320 from Patent EP1572962.
JD471929 - Sequence 452953 from Patent EP1572962.
JD057276 - Sequence 38300 from Patent EP1572962.
JD452462 - Sequence 433486 from Patent EP1572962.
JD345480 - Sequence 326504 from Patent EP1572962.
JD067225 - Sequence 48249 from Patent EP1572962.
JD316265 - Sequence 297289 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NMK4, IFITMD3, LOST1, NM_172367, NP_758955, Q8IXB3, TUSC5, TUSC5_HUMAN
UCSC ID: uc002fsi.1
RefSeq Accession: NM_172367
Protein: Q8IXB3 (aka TUSC5_HUMAN)
CCDS: CCDS42225.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_172367.2
exon count: 3CDS single in 3' UTR: no RNA size: 3596
ORF size: 534CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 869.00frame 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.