Caenorhabditis elegans essential complex locus dnj-9C, encoding DNaJ domain (prokaryotic heat shock protein).
SUMMARY back to top
[Wormbase] This gene encodes a protein containing a DnaJ ('J') domain.
Wormbase predicts 2 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 3 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 3.7 times the average gene in this release, at all stages of development [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 41%, L1 or L2 larvae 24%, L3 to adult 34%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 31 cDNA clones and 18 elements defined by RNA-seq, some from embryo (seen 9 times), l2 (4), l4 (2), l1 (once), mixed (once). We annotate structural defects or features in 2 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 9 distinct gt-ag introns. Transcription produces at least 5 different mRNAs, 3 alternatively spliced variants and 2 unspliced forms. Variant a is transpliced to SL1, b to SL1, c to SL2, SL1, SL3, SL4, SL5, d to SL1. There are 2 probable alternative promotors, 2 non overlapping alternative last exons and 8 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, overlapping exons with different boundaries.
Function: There are 2 articles specifically referring to this gene in PubMed. This essential gene is associated to a phenotype (Embryonic Lethal). Proteins are expected to localize in cytoplasm. These proteins appear to interact with other proteins (3G433, 4J607, 4L460, WWP-1).
Protein coding potential: 3 spliced mRNAs putatively encode good proteins, altogether 3 different isoforms (3 complete), some containing heat shock protein DnaJ, N-terminal domain [Pfam]. The remaining 2 mRNA variants (2 unspliced; 1 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 II, links to other databases and other names
Map: This essential gene dnj-9C maps on chomosome II at position -2.55 (interpolated). In AceView, it covers 7.10 kb, from 4852044 to 4859142 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
as Other names: The gene is also known dnj-9, in Wormgenes/AceView by its positional name 2F149, in Wormbase by its cosmid.number name F11G11.5, F11G11.7, in NextDB, the Nematode expression pattern database, as CEYK2332.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene DNAJC11 (e=2 10-25).
The closest mouse gene, according to BlastP, is the AceView gene Dnajc11 (e=5 10-25).
The closest A.thaliana genes, according to BlastP, are the AceView genes AT2G35720 (e=3 10-15), AT3G08910 (e=5 10-13), AT2G20560 (e=7 10-13)
          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 dnj-9C 5' 3' encoded on plus strand of chromosome II from 4,852,044 to 4,859,142 a c b e d 1 2kb 0 109 bp exon 109 bp exon 48 bp [gt-ag] intron 10 GenBank accessions 531 bp exon 47 bp [gt-ag] intron 9 GenBank accessions 142 bp exon 227 bp [gt-ag] intron 5 GenBank accessions 761 bp exon 360 bp [gt-ag] intron 9 GenBank accessions 130 bp exon 53 bp [gt-ag] intron 10 GenBank accessions 62 bp exon 62 bp exon 2915 bp [gt-ag] intron 9 GenBank accessions 32 accessions, some from embryo (seen 3 times) l2 (3), l4 (2), mixed (once) Transpliced 5' end, 5 accessions Validated 3' end, 1 accession Validated 3' end, 7 accessions 367 bp exon 55 bp exon 55 bp exon 92 bp [gt-ag] intron 8 GenBank accessions 352 bp exon 101 bp [gt-ag] intron 9 GenBank accessions 122 bp exon 50 bp [gt-ag] intron 9 GenBank accessions 460 bp exon 13 accessions, some from embryo (seen 6 times) l1 (once) Transpliced 5' end, 2 accessions Validated 3' end, 27 accessions 460 bp exon 109 bp exon 109 bp exon 48 bp [gt-ag] intron 10 GenBank accessions 531 bp exon 47 bp [gt-ag] intron 9 GenBank accessions 89 bp exon Sequence gap 5349 bp 193 bp exon 101 bp [gt-ag] intron 9 GenBank accessions 122 bp exon 50 bp [gt-ag] intron 9 GenBank accessions 454 bp exon 1 accession from l2 Transpliced 5' end, 1 accession Validated 3' end, 22 accessions 454 bp exon 197 bp exon 197 bp exon 1 accession Validated 3' end, 3 accessions 197 bp exon 396 bp exon 396 bp exon 2 accessions Transpliced 5' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 3 accessions 396 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 5' UTR 3' UTR Upstream sequence Transcription
Downstream sequence
a 2102 bp 564 aa 406 bp 2kb including Promoter 5752 bp 1kb
b 2444 bp 713 aa 301 bp 2kb including Promoter 7093 bp 1kb
c 989 bp 223 aa 10 bp 307 bp 2kb including Promoter 1232 bp 1kb
d 396 bp 29 aa 183 bp 123 bp 2kb including Promoter 396 bp 1kb
e 197 bp 50 aa 43 bp 2kb 197 bp 1kb

Gene neighbors and Navigator on chromosome II back to top
2F125 C P nspd-4 C dnj-9C D C I R P 2F151 C I P P gst-6 D C P 2F145 2F124oh C 2F124 C P 2F126 D C P nspd-5 C P 2F152 D C I P col-17 D C I P col-20 C I P col-73 C 2F164 5kb 0 tbck-1, 16 accessions 2F125, 98 accessions nspd-4, 81 accessions dnj-9C, 49 accessions 5 variants 2F151, 6 accessions 2F155, 3 accessions gst-6, 22 accessions 2F141, 29 accessions, 2 variants 2F145, 0 accession 2F163, 5 accessions, 4 variants 2F124oh, 0 accession 2F132, 5 accessions 2F144, 1 accession 2F146, 2 accessions, 2 variants 2F166, 0 accession 2F124, 50 accessions, 2 variants 2F126, 18 accessions, 2 variants nspd-5, 55 accessions 2F152, 6 accessions col-17, 78 accessions 4 variants col-20, 130 accessions 4 variants col-73, 234 accessions 2 variants 2F164, 2 accessions 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.
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e Alternative mRNAs features, proteins, introns, exons, sequences 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 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'.

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