Biomaterial Database

Identification of novel splice variants of the human CD44 gene. 2006

Elena Vela, and Xavier Roca, and Marcos Isamat

Fundación Echevarne, Barcelona, Spain.

The CD44 gene contains 10 variable exons (v1-v10) that can be alternatively spliced to generate hundreds of different CD44 protein isoforms, several of which have been implicated in the metastatic spread of tumour cells. Here, we describe a cryptic splice site, in intron 6 of the human CD44 gene, used during mRNA processing. This cryptic splice site is used in conjunction with variable exon 3, or independently from it in the form of a pseudo-exon of 49 bp, which generates a stop codon by frame shift in the contiguous variable exon downstream. This pseudo-exon has been found inserted immediately 3' to any other variable exon from v4 to v10, in the final CD44 mRNA. The implication of this cryptic splice site in haltering CD44 protein translation is questioned in the context of Nonsense Mediated Decay and the overall regulation of CD44 expression.

UI	MeSH Term	Description	Entries
D009369	Neoplasms	New abnormal growth of tissue. Malignant neoplasms show a greater degree of anaplasia and have the properties of invasion and metastasis, compared to benign neoplasms.	Benign Neoplasm,Cancer,Malignant Neoplasm,Tumor,Tumors,Benign Neoplasms,Malignancy,Malignant Neoplasms,Neoplasia,Neoplasm,Neoplasms, Benign,Cancers,Malignancies,Neoplasias,Neoplasm, Benign,Neoplasm, Malignant,Neoplasms, Malignant
D002460	Cell Line	Established cell cultures that have the potential to propagate indefinitely.	Cell Lines,Line, Cell,Lines, Cell
D005091	Exons	The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.	Mini-Exon,Exon,Mini Exon,Mini-Exons
D006801	Humans	Members of the species Homo sapiens.	Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D012333	RNA, Messenger	RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.	Messenger RNA,Messenger RNA, Polyadenylated,Poly(A) Tail,Poly(A)+ RNA,Poly(A)+ mRNA,RNA, Messenger, Polyadenylated,RNA, Polyadenylated,mRNA,mRNA, Non-Polyadenylated,mRNA, Polyadenylated,Non-Polyadenylated mRNA,Poly(A) RNA,Polyadenylated mRNA,Non Polyadenylated mRNA,Polyadenylated Messenger RNA,Polyadenylated RNA,RNA, Polyadenylated Messenger,mRNA, Non Polyadenylated
D017398	Alternative Splicing	A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.	RNA Splicing, Alternative,Splicing, Alternative,Alternate Splicing,Nested Transcripts,Alternate Splicings,Alternative RNA Splicing,Alternative RNA Splicings,Alternative Splicings,Nested Transcript,RNA Splicings, Alternative,Splicing, Alternate,Splicing, Alternative RNA,Splicings, Alternate,Splicings, Alternative,Splicings, Alternative RNA,Transcript, Nested,Transcripts, Nested
D018389	Codon, Nonsense	An amino acid-specifying codon that has been converted to a stop codon (CODON, TERMINATOR) by mutation. Its occurance is abnormal causing premature termination of protein translation and results in production of truncated and non-functional proteins. A nonsense mutation is one that converts an amino acid-specific codon to a stop codon.	Codon, Termination, Premature,Codon, Unassigned,Mutation, Nonsense,Nonsense Codon,Nonsense Mutation,Premature Stop Codon,Unassigned Codon,Amber Nonsense Codon,Amber Nonsense Mutation,Nonsense Codon, Amber,Ochre Nonsense Codon,Ochre Nonsense Mutation,Opal Nonsense Codon,Opal Nonsense Mutation,Premature Termination Codon,Amber Nonsense Codons,Amber Nonsense Mutations,Codon, Amber Nonsense,Codon, Ochre Nonsense,Codon, Opal Nonsense,Codon, Premature Stop,Codon, Premature Termination,Codons, Amber Nonsense,Codons, Nonsense,Codons, Ochre Nonsense,Codons, Opal Nonsense,Codons, Premature Stop,Codons, Premature Termination,Codons, Unassigned,Mutation, Amber Nonsense,Mutation, Ochre Nonsense,Mutation, Opal Nonsense,Mutations, Amber Nonsense,Mutations, Nonsense,Mutations, Ochre Nonsense,Mutations, Opal Nonsense,Nonsense Codon, Ochre,Nonsense Codon, Opal,Nonsense Codons,Nonsense Codons, Amber,Nonsense Codons, Ochre,Nonsense Codons, Opal,Nonsense Mutation, Amber,Nonsense Mutation, Ochre,Nonsense Mutation, Opal,Nonsense Mutations,Nonsense Mutations, Amber,Nonsense Mutations, Ochre,Nonsense Mutations, Opal,Ochre Nonsense Codons,Ochre Nonsense Mutations,Opal Nonsense Codons,Opal Nonsense Mutations,Premature Stop Codons,Premature Termination Codons,Stop Codon, Premature,Stop Codons, Premature,Termination Codon, Premature,Termination Codons, Premature,Unassigned Codons
D018960	Hyaluronan Receptors	Acidic sulfated integral membrane glycoproteins expressed in several alternatively spliced and variable glycosylated forms on a wide variety of cell types including mature T-cells, B-cells, medullary THYMOCYTES; GRANULOCYTES; MACROPHAGES; erythrocytes, and fibroblasts. Their interaction with HYALURONIC ACID mediates binding of lymphocytes to high endothelial VENULES.	Antigens, CD44,CD44 Antigens,Hyaluronan-Binding Protein,Receptors, Hyaluronan,CD44 Antigen,Chondroitin Sulfate Proteoglycan 8,Hyaluronan Receptor,Hyaluronic Acid Binding Protein,Antigen, CD44,Hyaluronan Binding Protein,Receptor, Hyaluronan
D020033	Protein Isoforms	Different forms of a protein that may be produced from different GENES, or from the same gene by ALTERNATIVE SPLICING.	Isoform,Isoforms,Protein Isoform,Protein Splice Variant,Splice Variants, Protein,Protein Splice Variants,Isoform, Protein,Isoforms, Protein,Splice Variant, Protein,Variant, Protein Splice,Variants, Protein Splice
D020871	RNA Stability	The extent to which an RNA molecule retains its structural integrity and resists degradation by RNASE, and base-catalyzed HYDROLYSIS, under changing in vivo or in vitro conditions.	RNA Decay,mRNA Decay,mRNA Transcript Degradation,RNA Degradation,RNA Instability,mRNA Degradation,mRNA Instability,mRNA Stability,Decay, RNA,Decay, mRNA,Degradation, RNA,Degradation, mRNA,Degradation, mRNA Transcript,Instability, RNA,Instability, mRNA,Stability, RNA,Stability, mRNA,Transcript Degradation, mRNA