AceView: gene:hsp-16.2 a comprehensive annotation of human, mouse and worm genes with mRNAs or EST (2024)

Summary
[Rea et al, 2005] hsp-16.2 reporter predicts longevity in isogenic populations of C. elegans. On the first day of adult life, chance variation in the level of induction of a green fluorescent protein reporter coupled to the promoter from this gene predicts up to fourfold variations in subsequent survival. HSP-16.2 itself is probably not responsible for the observed effects but probably reflects a hidden, heterogeneous, but now quantifiable, physiological state that dictates the ability of an organism to deal with the rigors of living[Thierry-Mieg, WormGenes, 2005] hope this finding won't be used in an unethical way[Wormbase] hsp-16.2 encodes a 16-kD heat shock protein (HSP) that is a member of the hsp16/hsp20/alphaB-crystallin (HSP16) family of heat shock proteins; hsp-16.2 expression, strongest in intestine and pharynx, is induced in response to heat shock or other environmental stresses; HSP-16.2 has been shown to interact with intracellular human beta amyloid peptide, a primary component of the extracellular plaques found in Alzheimer's disease; HSP-16.2 is likely to function as a passive ligand temporarily preventing unfolded proteins from aggregating.
Wormbase predicts one model, but Caenorhabditis elegans cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 2 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 8.0 times the average gene in this release. The sequence of this gene is defined by 5 cDNA clones and 100 elements defined by RNA-seq, some from l1 (seen once). We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 2 distinct gt-ag introns. Transcription produces 2 alternatively spliced mRNAs. There are 6 validated alternative polyadenylation sites (see the diagram).
Function: There are 23 articles specifically referring to this gene in PubMed. In addition we point below to 19 abstracts. This gene is associated to a phenotype (overexpressed in the presence of cadmium, shared oogenic and spermatogenic protein copurified with chromatin). Proteins are expected to localize in nucleus. These proteins appear to interact with another protein (HSP-16.41).
Protein coding potential: The 2 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (1 complete, 1 COOH complete), some containing Heat shock protein Hsp20 domain [Pfam].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome V, links to other databases and other names
Map: This gene hsp-16.2 maps on chom*osome V at position -17.63 (interpolated). In AceView, it covers 0.65 kb, from 1804971 to 1804326 (WS190), on the reverse strand.
Links to: WormBase, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 5C282, in Wormbase by its cosmid.number name Y46H3A.3.
Closest AceView hom*ologs in other species ?
The closest human genes, according to BlastP, are the AceView genes CRYAB, HSPB1, CRYAA.
The closest mouse genes, according to BlastP, are the AceView genes Cryab (e=8 10^-14), Hspb1 (e=4 10^-11)

Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
Read more...

Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Details on tissue of origin for each intron and exon is available from the intron and exons table.
Click on any transcript to open the specific mRNA page, to see the exact cDNA clone support and eventual SNPs and to get details on tissues, sequences, mRNA and protein annotations. Proteins supported by a single continuous cDNA sequence lead to underlining the name/ending of the variant. Names not underlined result from cDNA concatenation in the coding region and should be experimentally checked.
Introns are depicted by broken lines; the height of the top of each intron reflects the relative number of clones supporting this intron. ]^[ A pink broken line denotes an intron with standard boundaries (gt-ag or gc-ag) that is exactly supported (i.e. a cDNA sequence exactly matches the genome over 16 bp, 8 on both sides of the intron). ] ^ ] A blue broken line denotes non-standard introns, exactly supported, but with non-standard at-ac or any other boundaries. ]-[ Pink and ] - ] blue straight lines represent 'fuzzy' introns of the standard and non-standard types respectively, those introns do not follow the 16 bp rule. Black straight lines ]-[denote gaps in the alignments.
Exons: Wide filled pink areas represent putative protein coding regions, narrow empty pink boxes represent the 5'UTR (on the left) and 3' UTR (on the right). Flags identify validated endings: cap site on the 5' side, polyadenylation site on the 3' side. Filled flags correspond to frequent events while empty flags have lesser supporting cDNAs (yet all are validated); at the 3' side, black flags are associated to the main AATAAA signal, blue flags to any single letter variant of the main . More explanations are given in the gene help file

Please see these 23 articles in PubMed.
In addition we found 19 papers for which we do not have a PubMed identifier

• pm19123269
• [wbg11.1p30] C elegans snRNA summary.
• [wbg11.2p25] STUDIES OF HSP-16 AND UBQ-1 EXPRESSION IN THE NEMATODE CAENORHABDITIS
• [wbg12.3p92] Forced Expression of the Tc3 ORF (Tc3A) Results in Tc3 Excision
• [wbg12.4p53] xol-1 Transcript Analysis and New 'Alleles'
• [wbg12.3p87] The Transposable Element Tc1 Encodes a Protein that Specifically Binds to Tc1 DNA Ends
• [wbg13.1p67] Genes in the lin-3/let-23 Signalling Pathway mediate the Signal From F/UDuring Development of the Male B Cell
• [wbg13.2p104] Site Directed Mutagenesis of the Tc3 Transposase Gene Suggests Functional Conservation Between Retro-Elements, IS Elements and the Tc1-Like Family
• [wbg13.5p81] age-1 Thermotolerance May Be Associated With hsp-16 Accumulation.
• [wm95p5] THE CONNECTION BETWEEN SL2-SPECIFIC TRANS-SPLICING AND 3' END FORMATION IN OPERONS
• [wm97e475] DETECTION OF A HER-1-BINDING PROTEIN IN C. ELEGANS EXTRACTS
• [wm97e367] PHYSIOLOGICAL EFFECTS OF BETA AMYLOID PEPTIDE EXPRESSION IN C. ELEGANS
• [wm97e110] STRESS RESISTANCE AND LIFE SPAN IN SELECTED STRAINS
• [wm97e68] gpa-12, A Gene Encoding a G12 Alpha Subunit
• [wm97e279] CHARACTERIZATION OF A STRESS-RESPONSIVE REPORTER TRANSGENE
• [mwwm98p94] Identification and analysis of genes involved in the control of cell polarity during C. elegans development.
• [wm99p207] G protein signaling pathways in C. elegans
• [wm2001p130] HEAT SHOCK TRANSCRIPTION FACTOR (HSF) ACTIVITY REGULATES THE APPEARANCE OF POLYGLUTAMINE PROTEIN AGGREGATES
• [wm2001p706] RNAi screen to identify genes involved in axon guidance
• [wm2001p636] Heat Shock Factor in C. elegans and in parasitic nematodes