Human Gene TM9SF4 (uc002wxj.2)
  Description: Homo sapiens transmembrane 9 superfamily protein member 4 (TM9SF4), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr20:30,697,309-30,755,061 Size: 57,753 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg19 chr20:30,697,544-30,753,247 Size: 55,704 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:30,697,309-30,755,061)mRNA (may differ from genome)Protein (642 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedTreefamUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TM9S4_HUMAN
DESCRIPTION: RecName: Full=Transmembrane 9 superfamily member 4; Flags: Precursor;
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (Probable).
SIMILARITY: Belongs to the nonaspanin (TM9SF) family.
SEQUENCE CAUTION: Sequence=AAH21107.1; Type=Erroneous initiation; Sequence=BAA13385.2; Type=Erroneous initiation;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: TM9SF4
Diseases sorted by gene-association score: melanoma (3)

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

+  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: 26.89 RPKM in Cells - Cultured fibroblasts
Total median expression: 933.68 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 -66.70235-0.284 Picture PostScript Text
3' UTR -611.521814-0.337 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
IPR004240 - EMP70

Pfam Domains:
PF02990 - Endomembrane protein 70

ModBase Predicted Comparative 3D Structure on Q92544
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 orthologGenome BrowserNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details  Gene DetailsGene Details
Gene SorterGene Sorter  Gene SorterGene Sorter
 RGD  WormBaseSGD
 Protein Sequence  Protein SequenceProtein Sequence
 Alignment  AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0001666 response to hypoxia
GO:0006909 phagocytosis
GO:0007155 cell adhesion
GO:0051453 regulation of intracellular pH
GO:0070072 vacuolar proton-transporting V-type ATPase complex assembly
GO:0070863 positive regulation of protein exit from endoplasmic reticulum
GO:2000010 positive regulation of protein localization to cell surface

Cellular Component:
GO:0005768 endosome
GO:0005769 early endosome
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK294980 - Homo sapiens cDNA FLJ54092 complete cds, highly similar to Transmembrane 9 superfamily protein member 4.
AK126534 - Homo sapiens cDNA FLJ44570 fis, clone UTERU3011063, highly similar to Transmembrane 9 superfamily protein member 4.
AK302439 - Homo sapiens cDNA FLJ54711 complete cds, highly similar to Transmembrane 9 superfamily protein member 4.
AK296500 - Homo sapiens cDNA FLJ53349 complete cds, highly similar to Transmembrane 9 superfamily protein member 4.
BC021107 - Homo sapiens transmembrane 9 superfamily protein member 4, mRNA (cDNA clone MGC:31858 IMAGE:4896167), complete cds.
D87444 - Homo sapiens mRNA for KIAA0255 gene, partial cds.
BC005173 - Homo sapiens cDNA clone IMAGE:3507918, containing frame-shift errors.
BC022850 - Homo sapiens transmembrane 9 superfamily protein member 4, mRNA (cDNA clone IMAGE:4098679), partial cds.
AB527227 - Synthetic construct DNA, clone: pF1KA0255, Homo sapiens TM9SF4 gene for transmembrane 9 superfamily protein member 4, without stop codon, in Flexi system.
AK316293 - Homo sapiens cDNA, FLJ79192 complete cds, highly similar to Transmembrane 9 superfamily protein member 4.
AK124411 - Homo sapiens cDNA FLJ42420 fis, clone BLADE2002730.
JD559948 - Sequence 540972 from Patent EP1572962.
JD485120 - Sequence 466144 from Patent EP1572962.
JD538920 - Sequence 519944 from Patent EP1572962.
JD312651 - Sequence 293675 from Patent EP1572962.
JD368194 - Sequence 349218 from Patent EP1572962.
JD228347 - Sequence 209371 from Patent EP1572962.
JD496150 - Sequence 477174 from Patent EP1572962.
JD457773 - Sequence 438797 from Patent EP1572962.
JD360862 - Sequence 341886 from Patent EP1572962.
JD230171 - Sequence 211195 from Patent EP1572962.
JD132919 - Sequence 113943 from Patent EP1572962.
JD166857 - Sequence 147881 from Patent EP1572962.
JD519560 - Sequence 500584 from Patent EP1572962.
JD164641 - Sequence 145665 from Patent EP1572962.
JD105137 - Sequence 86161 from Patent EP1572962.
JD513327 - Sequence 494351 from Patent EP1572962.
JD068560 - Sequence 49584 from Patent EP1572962.
JD103869 - Sequence 84893 from Patent EP1572962.
JD049677 - Sequence 30701 from Patent EP1572962.
JD073672 - Sequence 54696 from Patent EP1572962.
JD062243 - Sequence 43267 from Patent EP1572962.
JD330431 - Sequence 311455 from Patent EP1572962.
JD101686 - Sequence 82710 from Patent EP1572962.
JD324955 - Sequence 305979 from Patent EP1572962.
JD369383 - Sequence 350407 from Patent EP1572962.
JD455361 - Sequence 436385 from Patent EP1572962.
JD416739 - Sequence 397763 from Patent EP1572962.
JD190290 - Sequence 171314 from Patent EP1572962.
JD124119 - Sequence 105143 from Patent EP1572962.
JD511281 - Sequence 492305 from Patent EP1572962.
JD055374 - Sequence 36398 from Patent EP1572962.
JD053920 - Sequence 34944 from Patent EP1572962.
JD364788 - Sequence 345812 from Patent EP1572962.
JD513678 - Sequence 494702 from Patent EP1572962.
JD320093 - Sequence 301117 from Patent EP1572962.
JD566707 - Sequence 547731 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B0QYT7, KIAA0255, NM_014742, NP_055557, Q92544, Q9NUA3, TM9S4_HUMAN
UCSC ID: uc002wxj.2
RefSeq Accession: NM_014742
Protein: Q92544 (aka TM9S4_HUMAN or T9S4_HUMAN)
CCDS: CCDS13196.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014742.3
exon count: 18CDS single in 3' UTR: no RNA size: 3996
ORF size: 1929CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4019.00frame shift in genome: no % Coverage: 99.55
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.