Human Gene TMEM40 (ENST00000314124.12) from GENCODE V44
  Description: Homo sapiens transmembrane protein 40 (TMEM40), transcript variant 2, mRNA. (from RefSeq NM_018306)
Gencode Transcript: ENST00000314124.12
Gencode Gene: ENSG00000088726.16
Transcript (Including UTRs)
   Position: hg38 chr3:12,733,528-12,759,259 Size: 25,732 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg38 chr3:12,734,774-12,749,832 Size: 15,059 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr3:12,733,528-12,759,259)mRNA (may differ from genome)Protein (233 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
PubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Transmembrane protein 40;
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein.

-  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

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 49.75 RPKM in Esophagus - Mucosa
Total median expression: 127.46 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 -9.0077-0.117 Picture PostScript Text
3' UTR -423.301246-0.340 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
IPR026181 - TMEM40

ModBase Predicted Comparative 3D Structure on Q8WWA1
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane

-  Descriptions from all associated GenBank mRNAs
  AK092470 - Homo sapiens cDNA FLJ35151 fis, clone PLACE6010701.
AX747561 - Sequence 1086 from Patent EP1308459.
AK001898 - Homo sapiens cDNA FLJ11036 fis, clone PLACE1004289.
JD446220 - Sequence 427244 from Patent EP1572962.
JD076921 - Sequence 57945 from Patent EP1572962.
JD515394 - Sequence 496418 from Patent EP1572962.
JD457204 - Sequence 438228 from Patent EP1572962.
JD335410 - Sequence 316434 from Patent EP1572962.
JD443003 - Sequence 424027 from Patent EP1572962.
JD558808 - Sequence 539832 from Patent EP1572962.
JD118520 - Sequence 99544 from Patent EP1572962.
JD443002 - Sequence 424026 from Patent EP1572962.
JD235922 - Sequence 216946 from Patent EP1572962.
JD558807 - Sequence 539831 from Patent EP1572962.
JD201448 - Sequence 182472 from Patent EP1572962.
JD388470 - Sequence 369494 from Patent EP1572962.
JD335408 - Sequence 316432 from Patent EP1572962.
JD399963 - Sequence 380987 from Patent EP1572962.
JD052037 - Sequence 33061 from Patent EP1572962.
JD399962 - Sequence 380986 from Patent EP1572962.
JD208271 - Sequence 189295 from Patent EP1572962.
JD482674 - Sequence 463698 from Patent EP1572962.
JD199259 - Sequence 180283 from Patent EP1572962.
JD530375 - Sequence 511399 from Patent EP1572962.
JD557681 - Sequence 538705 from Patent EP1572962.
JD512386 - Sequence 493410 from Patent EP1572962.
JD412619 - Sequence 393643 from Patent EP1572962.
JD197718 - Sequence 178742 from Patent EP1572962.
JD267377 - Sequence 248401 from Patent EP1572962.
JD544068 - Sequence 525092 from Patent EP1572962.
JD532669 - Sequence 513693 from Patent EP1572962.
JD045324 - Sequence 26348 from Patent EP1572962.
JD470017 - Sequence 451041 from Patent EP1572962.
JD477283 - Sequence 458307 from Patent EP1572962.
JD544092 - Sequence 525116 from Patent EP1572962.
JD207256 - Sequence 188280 from Patent EP1572962.
JD341299 - Sequence 322323 from Patent EP1572962.
JD044610 - Sequence 25634 from Patent EP1572962.
JD521481 - Sequence 502505 from Patent EP1572962.
BC020658 - Homo sapiens transmembrane protein 40, mRNA (cDNA clone MGC:22330 IMAGE:4768606), complete cds.
JD068436 - Sequence 49460 from Patent EP1572962.
AK301984 - Homo sapiens cDNA FLJ55821 complete cds, highly similar to Homo sapiens transmembrane protein 40 (TMEM40), mRNA.
CU676614 - Synthetic construct Homo sapiens gateway clone IMAGE:100022140 5' read TMEM40 mRNA.
JD263933 - Sequence 244957 from Patent EP1572962.
KJ902805 - Synthetic construct Homo sapiens clone ccsbBroadEn_12199 TMEM40 gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000314124.1, ENST00000314124.10, ENST00000314124.11, ENST00000314124.2, ENST00000314124.3, ENST00000314124.4, ENST00000314124.5, ENST00000314124.6, ENST00000314124.7, ENST00000314124.8, ENST00000314124.9, NM_018306, Q8NAL4, Q8WWA1, Q9NUZ4, TMM40_HUMAN, uc003bxg.1, uc003bxg.2, uc003bxg.3, uc003bxg.4
UCSC ID: ENST00000314124.12
RefSeq Accession: NM_018306
Protein: Q8WWA1 (aka TMM40_HUMAN)
CCDS: CCDS2613.1

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