CDV3 (gene)

CDV3
Identifiers
Aliases	CDV3, H41, CDV3 homolog
External IDs	HomoloGene: 133862 GeneCards: CDV3
Gene location (Human) Chr. Chromosome 3 (human) Band 3q22.1 Start 133,573,686 bp End 133,590,261 bp
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in parietal pleura visceral pleura germinal epithelium corpus epididymis cancellous bone cavity of mouth vastus lateralis muscle glomerulus right ventricle tibia n/a More reference expression data BioGPS n/a
Gene ontology Molecular function molecular function Cellular component cytoplasm cytosol plasma membrane nucleolus Biological process cell population proliferation Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 55573 102639170 Ensembl ENSG00000091527 n/a UniProt Q9UKY7 n/a RefSeq (mRNA) NM_001134422 NM_001134423 NM_001282762 NM_001282763 NM_001282764 NM_001282765 NM_017548 n/a RefSeq (protein) NP_001127894 NP_001127895 NP_001269691 NP_001269692 NP_001269693 NP_001269694 NP_060018 n/a Location (UCSC) Chr 3: 133.57 – 133.59 Mb n/a PubMed search
Wikidata
View/Edit Human View/Edit Mouse

Protein CDV3 homolog also known as carnitine deficiency-associated gene expressed in ventricle 3 is a protein that in humans is encoded by the CDV3 gene.

CDV3 is a biomarker for hepatocellular carcinoma. CDV3 has been considered as a potential target for gene therapy. Related gene families include plasma proteins and predicted intracellular proteins.

Gene

Aliases

The CDV3 protein is also commonly known as tyrosine-phosphorylated protein 36 (TPP36). TPP36 isoforms have been found to be substrates of Abl tyrosine kinase.

Locus

The CDV3 gene is on chromosome 3 (3q22.1).

Chromosome location of CDV3 from NCBI Gene.

Exons

There were variations in the listed number of exons in CDV3 between genetic databases. The number of exons vary based on the isoform in question, with most transcript isoforms having 5 exons.

Span

The exons of human CDV3 gene's longest transcript isoform span 16,711 bp.

Transcripts

Isoforms

CDV3 has seven isoforms, and more are continuously added to databases as they are discovered. Currently there are isoforms a-f.

Protein

Molecular weight: 27.3 kD

Protein length: 258 aa

Isoelectric point: 5.89

Motifs

A SAPS analysis on the human CDV3 protein sequence found one uncharged cluster segment from 28-75 aa. There were no signs of high scoring hydrophobic segments. One high scoring transmembrane segment was found from 28-55 aa. CDV3 was found to have significant maximal spacing from 27-76 aa.

Repeats

The following repetitive structures were found for the protein.

Aligned matching blocks:

[45-52]  AGAAGGGA

[66-73]  AGAAGPGA

with superset:

  [32-36]   AGAAG

  [45-49]   AGAAG

  [  66- 70]   AGAAG

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[134-137]   MEKS

[213-216]   MEKS

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Simple tandem repeat:

[31-43]   AAGAA_GSAGGSSG

[44-54]   AAGAAGGGAGA

Predicted Motifs

PROSITE found several potential motifs in CDV3. 

Predicted Secondary Structure

Conceptual translation of the longest CDV3 isoform annotated with CDV3's predicted secondary structure and conserved amino acids.

The following programs were used to develop this figure: JPred, CFSSP, and GOR4. The majority of the CDV3 structure is hypothesized to be alpha helices and random coil.

Predicted 3D Structure

The 3D structure of CDV3 was predicted through amino acid submission to the Zhang Lab and their I-TASSER program.

Predicted CDV3 3D structure from I-TASSER.

Gene regulation

Promoter

There are currently six different predicted promoters based on supporting transcripts. The following promoters were found using Genomatix. Promoter GXP_141972 was chosen for further analysis because of the large number of supporting transcripts, and it was found to be conserved in 14 of 14 orth. loci.  

*No transcript assigned.

Expression patterns

CDV3 is ubiquitously expressed, and at relatively high levels, in all tissues examined in the humans. Higher expression existed in certain diseases.

Gene profile

Various experiments showing expression of CDV3 demonstrated different patterns of tissue expression; however, it is concluded that the gene is expressed ubiquitously throughout all tissue types with more expression within tissues involved in the immune system and skeletal muscle tissue.

HPA RNA-seq Normal Tissue Expression from NCBI Gene entry on CDV3.

The expression of CDV3 generally decreases throughout fetal development, but expression levels remain high.

Tissue-specific circular RNA induction during human fetal development from NCBI Gene entry on CDV3.

RNA sequencing of total RNA from 20 human tissues from NCBI Gene entry on CDV3.

Illumina bodyMap2 transcriptome from NCBI Gene entry on CDV3.

Protein Level Regulation

A conceptual translation was made from NCBI reference sequence NM_017548.4. Amino acids conserved in at least 70% of vertebrate orthologous proteins are bolded (seen in the section below).

A conceptual translation showing predicted sites of CDV3 protein regulation.

Evolution

Orthologs

The following orthologs were found through the NCBI database. The date of divergence between species and Homo sapies was determined using TimeTree. The sequence identity and similarity were found using BLAST.

Paralogs

No human paralogs were found for CDV3 GeneCards and GenesLikeMe databases through the Weizmann Institute of Science. There were not any other relevant sources when the Google Search was conducted.

Phylogenetic tree

A phylogenetic tree was developed from the species listed in the table above using "One Click Mode" on Phylogeny.fr.

Phylogenetic tree of species with CDV3 orthologs using Phylogeny.fr

Interacting proteins

Clinical significance

As earlier in the article, CDV3 has been found to be expressed in patients with various cancers and HIV. CDV3 has also been found to interact with Pr55 in the HIV retrovirus. Without further testing in expression, it is hard to determine how levels alter depending on disease state or the role this gene plays in these illnesses.