Caenorhabditis elegans gene hlh-3, encoding achaete-scute like, Helix Loop Helix protein interacting with HLH-2.
SUMMARY back to top
[Wormbase] hlh-3 encodes a basic helix-loop-helix transcription factor homologous to Drosophila Achaete-scute; in vitro, HLH-3 can heterodimerize, and bind an E-box-containing probe, with HLH-2, the C. elegans E/daughterless ortholog with which it is coexpressed in the nuclei of embryonic neuronal precursors.
Wormbase predicts one model

AceView synopsis, each blue text links to tables and details
According to AceView, this gene is expressed at very high level, 6.3 times the average gene in this release. The sequence of this gene is defined by 6 cDNA clones and 77 elements defined by RNA-seq, some from embryo (seen once).
The gene contains 1 gt-ag intron. Transcription produces one mRNA. Variant a is transpliced to SL1.
Function: There are 3 articles specifically referring to this gene in PubMed. In addition we point below to 5 abstracts. This gene is associated to a phenotype. Functionally, the gene has been proposed to participate in a process (regulation of transcription). Proteins are expected to have molecular function (transcription regulator activity) and to localize in various compartments (mitochondrion, nucleus). This protein appears to interact with another protein (HLH-2). The gene interacts with 2 other genes (CES-1, HLH-2).
The spliced mRNA putatively encodes a good protein, containing Basic helix-loop-helix dimerisation region bHLH domain [Pfam].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome II, links to other databases and other names
Map: This gene hlh-3 maps on chomosome II at position +1.18 (interpolated). In AceView, it covers 1.33 kb, from 9086528 to 9087858 (WS190), on the direct strand.
Links to: WormBase, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 2J377, in Wormbase by its cosmid.number name T24B8.6.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes ASCL4 (e=6 10-07), ASCL3 (e=2 10-06), PAH (e=7 10-06), ASCL1 (e=10-05).
The closest mouse genes, according to BlastP, are the AceView genes Ascl3 (e=2 10-06), Ascl1 (e=4 10-06), Ascl2 (e=7 10-05), Bhlhb8 (e=10-04).
The closest A.thaliana gene, according to BlastP, is the AceView gene UNE10 (e=2 10-04)
          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 hlh-3 5' 3' encoded on plus strand of chromosome II from 9,086,528 to 9,087,858 a 100 200bp 0 198 bp exon 198 bp exon 491 bp [gt-ag] intron 4 GenBank accessions 642 bp exon 83 accessions, some from embryo (seen once) Transpliced 5' end, 1 accession Validated 3' end, 570 accessions 642 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.
Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 3' UTR Upstream sequence Transcription
Downstream sequence
a 840 bp 170 aa 324 bp 2kb including Promoter 1331 bp 1kb

Gene neighbors and Navigator on chromosome II back to top
hlh-3 D C I P 2J391 D C P 2J401 C 2J395 2J364 C 2J354 D C I P 2J372 C 2J380 D C P clh-5 C I P dyrb-1 C I P dnj-23 5kb 0 hlh-3, 83 accessions 2J391, 8 accessions 2J401, 19 accessions, 2 variants 2J353, 1 accession 2J395, 6 accessions 2J364, 0 accession 2J354, 41 accessions, 15 variants 2J372, 10 accessions 2J380, 17 accessions, 5 variants clh-5, 21 accessions, 3 variants dyrb-1, 0 accession dnj-23, 228 accessions 5 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 3 articles in PubMed.
In addition we found 5 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA Expression Tissue Function, regulation, related genes DCI

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 see the mRNA diagram, sequence and annotation, click 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 !