Caenorhabditis elegans essential gene arx-7, encoding actin Related protein 2/3 compleX component.
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SUMMARY
Summary
[Wormbase] arx-7 encodes the C. elegans ortholog of the p16Arc subunit of the actin-related protein (Arp)2/3 complex
.
Wormbase predicts 4 models.
AceView summary
Expression: According to AceView, this gene is
expressed at high level, 3.9 times the average gene in this release, at all stages of development [Kohara cDNAs]. The
sequence of this gene is defined by
51 cDNA clones, some from whole animal (seen 2 times). We annotate
structural defects or features in 2 cDNA clones.
Alternative mRNA variants and regulation: The gene contains
15 distinct gt-ag introns. Transcription produces
4 alternatively spliced mRNAs. There are 2 non overlapping alternative last exons and 9 validated
alternative polyadenylation sites (see the
diagram). The mRNAs appear to differ by by truncation of the 3' end, presence or absence of 2
cassette exons. 88 bp of this gene
are antisense to spliced gene 1D637, raising the possibility of regulated alternate expression.
2 variants were isolated
in vivo, despite the fact that they are predicted targets of
nonsense mediated mRNA decay (NMD).
Protein coding potential: The 4 spliced mRNAs putatively encode
good proteins, altogether
6 different isoforms (3 complete, 5 COOH complete), some containing ARP2/3 complex 16 kDa subunit (p16-Arc)
domain [Pfam], a coiled coil stretch
[Psort2].
Function: There is
one article specifically referring to this gene in PubMed. This essential gene is associated to a
phenotype (Embryonic Lethal, Larval arrest, unhealthy, defective hypodermal enclosure). Functionally, the gene has been proposed to participate in a
process (regulation of actin polymerization). Proteins are expected to
localize in various compartments (nucleus, cytoskeleton).
Please quote:
AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12
Map on chromosome CHROMOSOME_I, links to other databases and other names
?
Map: This essential gene arx-7 maps on chomosome I at position -4.88 (interpolated). In AceView, it covers
15.56 kb, from 3084875 to 3069316 (WS190), on the reverse strand.
Links to: WormBase,
NextDB,
RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 1D638, in Wormbase by its cosmid.number name M01B12.3, M01B12.4, in NextDB, the Nematode expression pattern database, as CEYK2106.
Closest AceView homologs in other species
?
The closest human genes, according to BlastP, are the AceView genes
ARPC5 (e=10^-24),
ARPC5L (e=10^-22).
The closest mouse genes, according to BlastP, are the AceView genes
Arpc5 (e=10^-24),
Arpc5l (e=2 10^-20).
The closest A.thaliana genes, according to BlastP, are the AceView genes
CRK (e=7 10^-10),
AT5G65274 (e=6 10^-09)
Complete gene on genome diagram: (in true scale, with colored introns)
This diagram was in previous releases displayed by default on the right of the screen. It shows in true scale the gene on the genome, the mRNAs and the cDNA clones. Opening may be slow for large genes. Please choose between the
zoomable GIF version., and the
Flash version
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 cDNA clones supporting each intron. Superimposed introns of the same color are identical, of different colors are different.
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. 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. Details on tissue of origin for each intron and exon is available from the
intron and exons table. Good predicted proteins are in pink, yellow proteins may be partial or unconvincing, green are uORFs. Proteins supported by a single continuous GenBank accession 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.
More legend
Introns 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.
Exons: 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
What is known about the gene and its neighbors on chromosome CHROMOSOME_I
ZOOM OUT
D:disease,
C:conserved,
I:interactions,
R:regulation,
P:publications (see the
Legend)
ZOOM IN
D:disease,
C:conserved,
I:interactions,
R:regulation,
P:publications (see the
Legend)
Annotated mRNA diagrams
The mRNAs diagrams with the aligned cDNA sequence accessions and their mismatches are available in the mRNA pages accessible from the tab at the top of the page, or here:
In Flash:
.a, .b, .c, .d.
or in GIF:
.a, .b, .c, .d
To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function and 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 and 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 all variants, their summarized annotations, 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'.
If you know more about this gene, or found errors, please share your knowledge. Merci !