Human Gene CLPTM1 (ENST00000337392.10) from GENCODE V44
  Description: Homo sapiens CLPTM1 regulator of GABA type A receptor forward trafficking (CLPTM1), transcript variant 2, mRNA. (from RefSeq NM_001294)
Gencode Transcript: ENST00000337392.10
Gencode Gene: ENSG00000104853.16
Transcript (Including UTRs)
   Position: hg38 chr19:44,955,380-44,993,341 Size: 37,962 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg38 chr19:44,955,396-44,992,897 Size: 37,502 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:44,955,380-44,993,341)mRNA (may differ from genome)Protein (669 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CLPT1_HUMAN
DESCRIPTION: RecName: Full=Cleft lip and palate transmembrane protein 1;
FUNCTION: May play a role in T-cell development (By similarity).
INTERACTION: Q8VCW4:Unc93b1 (xeno); NbExp=2; IntAct=EBI-2873194, EBI-6116986;
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (Potential).
TISSUE SPECIFICITY: Widely expressed.
POLYMORPHISM: A chromosomal translocation involving CLPTM1 is found in a family with cleft lip and palate. However, no etiologic link with the disease is characterized. Translocation t(2;19)(q11.2;q13.3).
SIMILARITY: Belongs to the CLPTM1 family.
SEQUENCE CAUTION: Sequence=AAH04865.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing; Sequence=AAP35926.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing;

-  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: CLPTM1
Diseases sorted by gene-association score: cleft lip (47)

-  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: 73.17 RPKM in Adrenal Gland
Total median expression: 1727.09 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 -4.7016-0.294 Picture PostScript Text
3' UTR -189.70444-0.427 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
IPR008429 - CLPTM1

Pfam Domains:
PF05602 - Cleft lip and palate transmembrane protein 1 (CLPTM1)

ModBase Predicted Comparative 3D Structure on O96005
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-  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 BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsemblWormBase 
Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence 
AlignmentAlignmentAlignmentAlignmentAlignment 

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

Biological Process:
GO:0007275 multicellular organism development
GO:0030154 cell differentiation
GO:0033081 regulation of T cell differentiation in thymus

Cellular Component:
GO:0005887 integral component of plasma membrane
GO:0009897 external side of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK310826 - Homo sapiens cDNA, FLJ17868.
AK316094 - Homo sapiens cDNA, FLJ78993 complete cds, highly similar to Cleft lip and palate transmembrane protein 1.
AK293314 - Homo sapiens cDNA FLJ59465 complete cds, highly similar to Cleft lip and palate transmembrane protein 1.
AK304480 - Homo sapiens cDNA FLJ58081 complete cds, highly similar to Cleft lip and palate transmembrane protein 1.
LF384224 - JP 2014500723-A/191727: Polycomb-Associated Non-Coding RNAs.
MA619801 - JP 2018138019-A/191727: Polycomb-Associated Non-Coding RNAs.
BC004865 - Homo sapiens cleft lip and palate associated transmembrane protein 1, mRNA (cDNA clone MGC:10593 IMAGE:3840991), complete cds.
AK223553 - Homo sapiens mRNA for cleft lip and palate associated transmembrane protein 1 variant, clone: FCC126F08.
AK074935 - Homo sapiens cDNA FLJ90454 fis, clone NT2RP3001560, highly similar to Cleft lip and palate transmembrane protein 1.
AK075262 - Homo sapiens cDNA FLJ90781 fis, clone THYRO1001242, highly similar to Homo sapiens cleft lip and palate transmembrane protein 1 (CLPTM1) mRNA.
AF037339 - Homo sapiens cleft lip and palate transmembrane protein 1 (CLPTM1) mRNA, complete cds.
BC012359 - Homo sapiens cleft lip and palate associated transmembrane protein 1, mRNA (cDNA clone MGC:20444 IMAGE:4685026), complete cds.
CU680306 - Synthetic construct Homo sapiens gateway clone IMAGE:100017445 5' read CLPTM1 mRNA.
DQ895436 - Synthetic construct Homo sapiens clone IMAGE:100009896; FLH184387.01L; RZPDo839F05143D cleft lip and palate associated transmembrane protein 1 (CLPTM1) gene, encodes complete protein.
KJ905716 - Synthetic construct Homo sapiens clone ccsbBroadEn_15386 CLPTM1 gene, encodes complete protein.
DQ892236 - Synthetic construct clone IMAGE:100004866; FLH184391.01X; RZPDo839F05144D cleft lip and palate associated transmembrane protein 1 (CLPTM1) gene, encodes complete protein.
KU177986 - Homo sapiens cleft lip and palate associated transmembrane protein 1 isoform 1 (CLPTM1) mRNA, partial cds, alternatively spliced.
KU177987 - Homo sapiens cleft lip and palate associated transmembrane protein 1 isoform 2 (CLPTM1) mRNA, complete cds.
BT007262 - Homo sapiens cleft lip and palate associated transmembrane protein 1 mRNA, complete cds.
KJ896619 - Synthetic construct Homo sapiens clone ccsbBroadEn_06013 CLPTM1 gene, encodes complete protein.
JD436564 - Sequence 417588 from Patent EP1572962.
LF367000 - JP 2014500723-A/174503: Polycomb-Associated Non-Coding RNAs.
MA602577 - JP 2018138019-A/174503: Polycomb-Associated Non-Coding RNAs.
LF366997 - JP 2014500723-A/174500: Polycomb-Associated Non-Coding RNAs.
MA602574 - JP 2018138019-A/174500: Polycomb-Associated Non-Coding RNAs.
LF366996 - JP 2014500723-A/174499: Polycomb-Associated Non-Coding RNAs.
MA602573 - JP 2018138019-A/174499: Polycomb-Associated Non-Coding RNAs.
LF366994 - JP 2014500723-A/174497: Polycomb-Associated Non-Coding RNAs.
MA602571 - JP 2018138019-A/174497: Polycomb-Associated Non-Coding RNAs.
LF366989 - JP 2014500723-A/174492: Polycomb-Associated Non-Coding RNAs.
MA602566 - JP 2018138019-A/174492: Polycomb-Associated Non-Coding RNAs.
LF366988 - JP 2014500723-A/174491: Polycomb-Associated Non-Coding RNAs.
MA602565 - JP 2018138019-A/174491: Polycomb-Associated Non-Coding RNAs.
LF366987 - JP 2014500723-A/174490: Polycomb-Associated Non-Coding RNAs.
MA602564 - JP 2018138019-A/174490: Polycomb-Associated Non-Coding RNAs.
AK027698 - Homo sapiens cDNA FLJ14792 fis, clone NT2RP4001149, highly similar to Homo sapiens cleft lip and palate transmembrane protein 1 (CLPTM1) mRNA.
LF366984 - JP 2014500723-A/174487: Polycomb-Associated Non-Coding RNAs.
MA602561 - JP 2018138019-A/174487: Polycomb-Associated Non-Coding RNAs.
LF366983 - JP 2014500723-A/174486: Polycomb-Associated Non-Coding RNAs.
MA602560 - JP 2018138019-A/174486: Polycomb-Associated Non-Coding RNAs.
JD142248 - Sequence 123272 from Patent EP1572962.
JD391955 - Sequence 372979 from Patent EP1572962.
JD484758 - Sequence 465782 from Patent EP1572962.
JD496689 - Sequence 477713 from Patent EP1572962.
JD161317 - Sequence 142341 from Patent EP1572962.
JD085229 - Sequence 66253 from Patent EP1572962.
JD437122 - Sequence 418146 from Patent EP1572962.
JD446029 - Sequence 427053 from Patent EP1572962.
JD390286 - Sequence 371310 from Patent EP1572962.
JD056225 - Sequence 37249 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: CLPT1_HUMAN, ENST00000337392.1, ENST00000337392.2, ENST00000337392.3, ENST00000337392.4, ENST00000337392.5, ENST00000337392.6, ENST00000337392.7, ENST00000337392.8, ENST00000337392.9, NM_001294, O96005, Q53ET6, Q9BSS5, uc002pai.1, uc002pai.2, uc002pai.3, uc002pai.4, uc002pai.5, uc002pai.6
UCSC ID: ENST00000337392.10
RefSeq Accession: NM_001294
Protein: O96005 (aka CLPT1_HUMAN)
CCDS: CCDS12651.1, CCDS74394.1

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