Human Gene CLPTM1 (uc021uvo.1)
  Description: Homo sapiens cleft lip and palate associated transmembrane protein 1 (CLPTM1), transcript variant 3, non-coding RNA.
Transcript (Including UTRs)
   Position: hg19 chr19:45,495,491-45,496,598 Size: 1,108 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr19:45,495,502-45,496,307 Size: 806 Coding Exon Count: 2 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:45,495,491-45,496,598)mRNA (may differ from genome)Protein (217 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSEnsemblExonPrimerGeneCardsH-INVHGNC
LynxMalacardsMGIPubMedTreefamWikipedia

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CLPTM1
CDC HuGE Published Literature: CLPTM1

-  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

+  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: 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
3' UTR -116.30291-0.400 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.

-  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 orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  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.
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.
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.
MA619801 - JP 2018138019-A/191727: 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.
LF366983 - JP 2014500723-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.
MA602561 - JP 2018138019-A/174487: Polycomb-Associated Non-Coding RNAs.
MA602560 - JP 2018138019-A/174486: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: AK027698
UCSC ID: uc021uvo.1
RefSeq Accession: NR_040006

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK027698.1
exon count: 2CDS single in 3' UTR: no RNA size: 921
ORF size: 654CDS single in intron: no Alignment % ID: 99.89
txCdsPredict score: 854.00frame 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.