[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.
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
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
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
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
The closest mouse genes
, according to BlastP, are the AceView genes Ascl3
The closest A.thaliana gene
, according to BlastP, is the AceView gene UNE10
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.
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.
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.
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