Caenorhabditis elegans essential gene apn-1, encoding endonuclease IV, has intrinsic apurinic/apyrimidinic endonuclease and 3'-diesterase activities; affects base excision repair.
SUMMARY back to top
[Wormbase] apn-1 encodes a member of the AP (apurinic or apyrimidinic) endonuclease family.
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 2 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 1.9 times the average gene in this release, 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 1%, L1 or L2 larvae 21%, L3 to adult (including dauer) 78%. The sequence of this gene is defined by 8 cDNA clones and 17 elements defined by RNA-seq, some from mixed (seen 2 times), l2 (once). We annotate structural defects or features in 8 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 2 distinct gt-ag introns. Transcription produces 2 alternatively spliced mRNAs. Variant a is transpliced to SL3, SL2, SL1, SL4, SL5. There are 2 probable alternative promotors and 5 validated alternative polyadenylation sites (see the diagram). 420 bp of this gene are antisense to spliced gene 2I340, raising the possibility of regulated alternate expression.
Function: There are 5 articles specifically referring to this gene in PubMed. In addition we point below to one abstract. This essential gene is associated to a phenotype (affects base excision repair, embryonic lethal, partial). Proteins are expected to localize in cytoplasm.
Protein coding potential: The 2 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (2 complete), some containing Xylose isomerase-type TIM barrel 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 essential gene apn-1 maps on chomosome II at position +0.57 (interpolated). In AceView, it covers 1.90 kb, from 8047494 to 8049389 (WS190), on the direct strand.
Links to: WormBase, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 2I339, in Wormbase by its cosmid.number name T05H10.2.
          Complete gene on genome diagram: back to top
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This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene apn-1 5' 3' encoded on plus strand of chromosome II from 8,047,494 to 8,049,071 a b 500bp 0 145 bp exon 212 bp [gt-ag] intron 4 GenBank accessions 630 bp exon 51 bp [gt-ag] intron 7 GenBank accessions 454 bp exon 8 accessions, some from mixed (seen 2 times) l2 (once) Transpliced 5' end, 3 accessions Validated 3' end, 17 accessions 454 bp exon 657 bp exon 657 bp exon 51 bp [gt-ag] intron 7 GenBank accessions 858 bp exon 17 accessions Validated 3' end, 16 accessions Validated 3' end, 60 accessions Validated 3' end, 41 accessions Validated 3' end, 25 accessions 858 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 1229 bp 396 aa 38 bp 2kb including Promoter 1492 bp 1kb
b 1515 bp 278 aa 236 bp 442 bp 2kb possibly including promoter 1566 bp 1kb

Gene neighbors and Navigator on chromosome II back to top
2I333 C 2I337 C R P apn-1 D C R P 2I343 C R P 2I349 C ufd-2 D C I R P D C R P D C R P 2I314 D C P nrf-6 D C I R P sap-49C D C I R P ubh-4 C R 2I340 C R 2I358 5kb 0 2I333, 8 accessions, 2 variants 2I337, 45 accessions, 2 variants apn-1, 25 accessions, 2 variants 2I343, 29 accessions, 4 variants 2I349, 9 accessions ufd-2, 159 accessions 9 variants 2I357, 0 accession 2I314, 73 accessions, 4 variants nrf-6, 34 accessions, 2 variants sap-49C, 110 accessions 8 variants ubh-4, 16 accessions, 4 variants 2I340, 37 accessions 2I358, 47 accessions, 3 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 5 articles in PubMed.
In addition we found 1 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DC

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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