Caenorhabditis elegans gene hum-2, encoding heavy chain, Unconventional Myosin.
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SUMMARY back to top
Summary
[Wormbase] hum-2 is orthologous to the human gene MYOSIN HEAVY CHAIN 12 (MYO5A; OMIM:160777), which when mutated leads to disease.
Wormbase predicts 5 models, 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 10 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 6.0 times the average gene in this release, mostly from L1 larvae to adult [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 3%, L1 or L2 larvae 35%, L3 to adult 61%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 33 cDNA clones and 46 elements defined by RNA-seq, some from mixed (seen 12 times), l2 (9), l1 (6), embryo (once). We annotate structural defects or features in 2 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 21 distinct introns (20 gt-ag, 1 gc-ag). Transcription produces at least 11 different mRNAs, 10 alternatively spliced variants and 1 unspliced form. Variant d is transpliced to SL1, e to SL1', f to SL1, SL2, SL3, SL4, SL6, g to SL1, k to SL1. There are 5 probable alternative promotors, 3 non overlapping alternative last exons and 7 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of a cassette exon, overlapping exons with different boundaries, splicing versus retention of one intron.
Note that mRNA .h was found in vivo, although it is a predicted target of nonsense mediated mRNA decay (NMD).
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant e).
Function: There are 2 articles specifically referring to this gene in PubMed. In addition we point below to 3 abstracts. Proteins are expected to have molecular functions (ATP binding activity, motor activity) and to localize in myosin. These proteins appear to interact with another protein (1O383).
Protein coding potential: 9 spliced mRNAs putatively encode good proteins, altogether 9 different isoforms (5 complete, 3 COOH complete, 1 partial), some containing domains Dilute, IQ calmodulin-binding region, Myosin head, motor region [Pfam], a coiled coil stretch [Psort2]. The remaining 2 mRNA variants (1 spliced, 1 unspliced; 2 partial) appear not to encode good proteins.

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 hum-2 maps on chomosome V at position +1.89 (interpolated). In AceView, it covers 13.93 kb, from 9386127 to 9400051 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 5J879, in Wormbase by its cosmid.number name F36D4.3, in NextDB, the Nematode expression pattern database, as CEYK190.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes MYO5BandACAA2, MYO5A, MYO5C.
The closest mouse genes, according to BlastP, are the AceView genes Myo5b (e=0.0), Myo5a (e=0.0), Myo5c (e=0.0).
The closest A.thaliana genes, according to BlastP, are the AceView genes MYA1, MYA2, XIC, XIK, XIH, XIF, XIA, XIB, XI-I, XIE, XID, XIG, XIJ, ATATM, VIIIA, PUX1
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene hum-2 5' 3' encoded on plus strand of chromosome V from 9,386,127 to 9,400,051 a k b c d e j f g h i 5kb 0 133 bp exon 133 bp exon 97 bp [gt-ag] intron 1 GenBank accession 114 bp exon 49 bp [gt-ag] intron 2 GenBank accessions 518 bp exon 50 bp [gt-ag] intron 2 GenBank accessions 1927 bp exon 49 bp [gt-ag] intron 4 GenBank accessions 150 bp exon 47 bp [gt-ag] intron 5 GenBank accessions 90 bp exon 2493 bp [gt-ag] intron 6 GenBank accessions 95 bp exon 463 bp [gt-ag] intron 7 GenBank accessions 142 bp exon 601 bp [gt-ag] intron 2 GenBank accessions 256 bp exon 46 bp [gt-ag] intron 6 GenBank accessions 601 bp exon 48 bp [gt-ag] intron 9 GenBank accessions 88 bp exon 2536 bp [gt-ag] intron 8 GenBank accessions 78 bp exon 43 bp [gt-ag] intron 14 GenBank accessions 88 bp exon 1357 bp [gt-ag] intron 10 GenBank accessions 117 bp exon 69 bp [gt-ag] intron 13 GenBank accessions 682 bp exon 51 bp [gt-ag] intron 14 GenBank accessions 301 bp exon 46 bp [gt-ag] intron 26 GenBank accessions 486 bp exon 48 accessions, some from mixed (seen 4 times) l1 (3), embryo (once) l2 (once) Validated 3' end, 1 accession Validated 3' end, 73 accessions 486 bp exon 106 bp exon 1 accession Transpliced 5' end, 1 accession 106 bp exon 6 bp exon 49 bp [gt-ag] intron 4 GenBank accessions 150 bp exon 47 bp [gt-ag] intron 5 GenBank accessions 90 bp exon 2493 bp [gt-ag] intron 6 GenBank accessions 95 bp exon 463 bp [gt-ag] intron 7 GenBank accessions 142 bp exon 607 bp [gt-ag] intron 6 GenBank accessions 250 bp exon 46 bp [gt-ag] intron 6 GenBank accessions 601 bp exon 48 bp [gt-ag] intron 9 GenBank accessions 88 bp exon 2536 bp [gt-ag] intron 8 GenBank accessions 78 bp exon 43 bp [gt-ag] intron 14 GenBank accessions 88 bp exon 1357 bp [gt-ag] intron 10 GenBank accessions 117 bp exon 69 bp [gt-ag] intron 13 GenBank accessions 682 bp exon 51 bp [gt-ag] intron 14 GenBank accessions 301 bp exon 46 bp [gt-ag] intron 26 GenBank accessions 486 bp exon 5 accessions, some from mixed (seen 4 times) Validated 3' end, 53 accessions 486 bp exon 710 bp exon 710 bp exon 66 bp [gc-ag] intron 7 GenBank accessions 78 bp exon 43 bp [gt-ag] intron 14 GenBank accessions 88 bp exon 1357 bp [gt-ag] intron 10 GenBank accessions 117 bp exon 69 bp [gt-ag] intron 13 GenBank accessions 682 bp exon 51 bp [gt-ag] intron 14 GenBank accessions 301 bp exon 46 bp [gt-ag] intron 26 GenBank accessions 481 bp exon 5 accessions, some from l1 (seen 2 times) mixed (once) 481 bp exon 182 bp exon 182 bp exon 66 bp [gc-ag] intron 7 GenBank accessions 78 bp exon 43 bp [gt-ag] intron 14 GenBank accessions 88 bp exon 1357 bp [gt-ag] intron 10 GenBank accessions 117 bp exon 69 bp [gt-ag] intron 13 GenBank accessions 682 bp exon 51 bp [gt-ag] intron 14 GenBank accessions 301 bp exon 46 bp [gt-ag] intron 26 GenBank accessions 481 bp exon 5 accessions, some from l2 (seen 3 times) mixed (once) Transpliced 5' end, 5 accessions 481 bp exon 326 bp exon 326 bp exon 165 bp uORF 326 bp exon 326 bp exon 43 bp [gt-ag] intron 14 GenBank accessions 88 bp exon 88 bp exon 1357 bp [gt-ag] intron 10 GenBank accessions 117 bp exon 117 bp exon 69 bp [gt-ag] intron 13 GenBank accessions 682 bp exon 682 bp exon 51 bp [gt-ag] intron 14 GenBank accessions 301 bp exon 301 bp exon 46 bp [gt-ag] intron 26 GenBank accessions 478 bp exon 478 bp exon 1 accession from l1 Transpliced 5' end, 1 accession 478 bp exon 83 bp exon 1491 bp [gt-ag] intron 1 GenBank accession 979 bp exon 1 accession 979 bp exon 117 bp exon 69 bp [gt-ag] intron 13 GenBank accessions 682 bp exon 682 bp exon 51 bp [gt-ag] intron 14 GenBank accessions 301 bp exon 46 bp [gt-ag] intron 26 GenBank accessions 500 bp exon 9 accessions, some from l2 (seen 5 times) mixed (once) Transpliced 5' end, 4 accessions Validated 3' end, 55 accessions 500 bp exon 95 bp exon 95 bp exon 463 bp [gt-ag] intron 7 GenBank accessions 142 bp exon 607 bp [gt-ag] intron 6 GenBank accessions 250 bp exon 46 bp [gt-ag] intron 6 GenBank accessions 255 bp exon Sequence gap 3306 bp 839 bp exon 2 accessions, some from mixed (seen once) Transpliced 5' end, 1 accession 839 bp exon 576 bp exon 576 bp exon 869 bp [gt-ag] intron 1 GenBank accession 1 accession 114 bp exon 1293 bp exon 1293 bp exon 1293 bp exon 152 bp [gt-ag] intron 1 GenBank accession 114 bp exon 114 bp exon 1 accession 114 bp exon 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.
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Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
a 5866 bp 1836 aa 354 bp 2kb 13911 bp 1kb
b 3174 bp 939 aa 354 bp 2kb 11029 bp 1kb
c 2457 bp 548 aa 461 bp 349 bp 2kb 4089 bp 1kb
d 1929 bp 516 aa 29 bp 349 bp 2kb including Promoter 3561 bp 1kb
e 1992 bp 440 aa 323 bp 346 bp 162 bp 2kb including Promoter 3558 bp 1kb
f 1600 bp 391 aa 479 bp 368 bp 2kb including Promoter 1766 bp 1kb
g 2104 bp 492 aa 78 bp 547 bp 2kb including Promoter 6003 bp 1kb
h 690 bp 152 aa 231 bp 2kb 1559 bp 1kb
i 1407 bp 66 aa 1208 bp 2kb possibly including promoter 1559 bp 1kb
j 1062 bp 43 aa 930 bp 2kb 2553 bp 1kb
k 106 bp 19 aa 49 bp 2kb including Promoter 106 bp 1kb

Gene neighbors and Navigator on chromosome V back to top
hum-2 C I R P 5J881 C I P 5J886 5J890 C 5J850 C R 5J852 D C I P 5J854 C 5J856 C R 5J862 C 5J860 C 5J882 5kb 0 hum-2, 79 accessions, 11 variants 5J881, 11 accessions, 2 variants 5J886, 0 accession 5J890, 0 accession 5J894, 0 accession 5J850, 6 accessions 5J852, 19 accessions, 11 variants 5J854, 0 accession 5J856, 4 accessions 5J862, 25 accessions, 2 variants 5J860, 0 accession 5J882, 21 accessions, 4 variants ZOOM OUT                 D:disease, C:conserved, I:interactions, R:regulation, P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography back to top
Please see these 2 articles in PubMed.
In addition we found 3 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i, .j, .k Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes CI

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !