Caenorhabditis elegans gene gly-3, encoding GLYcosylation related protein.
SUMMARY back to top
[Wormbase] gly-3 encodes an N-acetylgalactosaminyltransferase that is functional in vitro.
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 3 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 5.2 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 51%, L3 to adult (including dauer) 46%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 39 cDNA clones and 29 elements defined by RNA-seq, some from l2 (seen 16 times), l1 (6), mixed (4), l4 (3), embryo (once). We annotate structural defects or features in 6 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 8 distinct gt-ag introns. Transcription produces 3 alternatively spliced mRNAs. Variant a is transpliced to SL2, SL7, SL3, SL4, SL11. There are 5 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by presence or absence of a cassette exon, overlapping exons with different boundaries.
Function: There are 2 articles specifically referring to this gene in PubMed. In addition we point below to 2 abstracts. Proteins are expected to localize in membrane. No phenotype has yet been reported to our knowledge: this gene's in vivo function is yet unknown.
Protein coding potential: The 3 spliced mRNAs putatively encode good proteins, altogether 3 different isoforms (1 complete, 1 COOH complete, 1 partial), some containing domains Glycosyl transferase, family 2, ricin B lectin [Pfam].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome III, links to other databases and other names
Map: This gene gly-3 maps on chomosome III at position -0.37 (interpolated). In AceView, it covers 3.47 kb, from 7917696 to 7914223 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 3J4, in Wormbase by its cosmid.number name ZK688.8, in NextDB, the Nematode expression pattern database, as CEYK4187.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes GALNT1 (e= 10-119), GALNT13 (e= 10-117).
The closest mouse genes, according to BlastP, are the AceView genes Galnt1 (e= 10-166), Galnt13 (e= 10-162)
          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 gly-3 5' 3' encoded on minus strand of chromosome III from 7,917,696 to 7,914,223 a b c 1kb 0 155 bp exon 155 bp exon 48 bp [gt-ag] intron 28 GenBank accessions 155 bp exon 52 bp [gt-ag] intron 27 GenBank accessions 386 bp exon 183 bp [gt-ag] intron 21 GenBank accessions 873 bp exon 774 bp [gt-ag] intron 24 GenBank accessions 150 bp exon 112 bp [gt-ag] intron 29 GenBank accessions 586 bp exon 63 accessions, some from l2 (seen 15 times) l1 (6), mixed (4), l4 (3) Transpliced 5' end, 24 accessions Validated 3' end, 80 accessions 586 bp exon 873 bp exon 768 bp [gt-ag] intron 3 GenBank accessions 156 bp exon 112 bp [gt-ag] intron 29 GenBank accessions 571 bp exon 3 accessions, some from embryo (seen once) l2 (once) Validated 3' end, 2 accessions Validated 3' end, 2 accessions Validated 3' end, 2 accessions Validated 3' end, 33 accessions 571 bp exon 873 bp exon 535 bp [gt-ag] intron 1 GenBank accession 93 bp exon 146 bp [gt-ag] intron 1 GenBank accession 2 accessions 150 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 2305 bp 612 aa 9 bp 457 bp 2kb including Promoter 3474 bp 1kb
b 1600 bp 385 aa 442 bp 2kb 2480 bp 1kb
c 1116 bp 372 aa 2kb 1797 bp 1kb

Gene neighbors and Navigator on chromosome III back to top
3I983 C R 3I993 C 3J1 C C npp-15 D C P ran-2 D C R P 3J27 C R 3I985 P C pcp-5 C 3J2 C R P gly-3 C I P 3J8 C R 3J16 5kb 0 3I983, 28 accessions, 5 variants 3I993, 30 accessions, 2 variants 3J1, 8 accessions 3J9, 16 accessions npp-15, 60 accessions 3 variants ran-2, 54 accessions, 6 variants 3J27, 13 accessions, 3 variants 3I985, 0 accession 3J11, 2 accessions 3I998, 11 accessions 3I976, 40 accessions, 5 variants 3I986, 9 accessions, 2 variants pcp-5, 98 accessions, 3 variants 3J2, 7 accessions gly-3, 68 accessions, 3 variants 3J8, 32 accessions, 5 variants 3J16, 36 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 2 articles in PubMed.
In addition we found 2 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes C

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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