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reconstructed by co-alignment and clustering of all publicly available
mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable
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Caenorhabditis elegans gene rrt-2, encoding aRginyl aa-tRNA syntheTase.
TABLE OF CONTENTS / OPEN CLOSE ALL PARAGRAPHS
Compact gene diagram
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.
Read more...
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.
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
Expression and GenBank cDNA support
Tissues where expression was observed (from 13 cDNA clones)
Origin of the cDNAs, as reported in GenBank/dbEST (tissue, stage, pathological or normal) shows that the gene is expressed in whole animal (seen 15 times).
Libraries: Kohara embryonic lambda gt11 library: yk427e6, yk281h12;
Kohara Sugano L1 larvae cap-selected library: yk1162b4, yk1275d4;
Kohara Sugano L2 larvae cap-selected library: yk1756a10, yk1522a5, yk1506b2, yk1406a4;
Kohara Sugano mixed stage cap-selected library: yk703c1, yk741f5;
Exelixis: 1764179, 1784678;
Marc Vidal ORFeome library [Nat Genet. 2003 May;34(1):35-41]: OST_10027F5.
Expression
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The
expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 15%, L1 or L2 larvae 45%, L3 to adult (including dauer) 40%.
In situ hybridisation pictures to all stages of development are available from Kohara NextDB (may be slow, but please be patient, it is worth it !). Note that this extraordinary resource is still unpublished: Users of the data presented on the NextDB web pages should not publish the information without
Kohara's permission and appropriate acknowledgment. They also appreciate any suggestions and comments.
13 cDNA clones support the 2 variants of gene rrt-2
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This table helps analyze the pattern of expression of the gene, the tissue, cell type or disease state specificity of the alternative variants and to select cDNA clones suitable for your experiments.
cDNA accession Links to the sequence |
Tissue
most 5' clones in red |
Match mRNA |
From bp to bp in mRNA |
From bp to bp in accs. |
Features |
Anomalies detected by AceView |
Accession match over (% length) |
Base differences relative to genome (% identity) |
EX1764179 | | .a | 76 to 537 | 174 to 638 | | | 465/715 (65 %) | 36 diff (95.0 %id) |
GB:EC032778 | | .a | 246 to 377 | 1 to 132 | | | 132/132 (100 %) | 4 diff (97.0 %id) |
EX1784678_3 | | .a | 955 to 1514 | 118 to 677 | fully sequenced, | Submitted on the opposite strand | 560/560 (100 %) | 1 diff (99.9 %id) |
EX1784678_5 | | .a | 1484 to 1766 | 346 to 62 | fully sequenced, | Submitted on the opposite strand | 285/346 (82 %) | 8 diff (97.7 %id) |
OSTF_10027F5 | whole animal | .a | 2 to 757 | 143 to 888 | | | 746/790 (94 %) | 32 diff (96.0 %id) |
OSTR027F5_2 | whole animal | .a | 973 to 1537 | 688 to 124 | | | 565/566 (99 %) | 10 diff (98.3 %id) |
yk281h12.3 | | .a | 1057 to 1753 | 697 to 1 | | | 697/930 (74 %) | 0 diff (100 %id) |
yk281h12.5 | | .a | 23 to 680 | 23 to 680 | | | 658/659 (99 %) | 1 diff (99.9 %id) |
yk427e6.3 | | .a | 1103 to 1763 | 661 to 1 | | | 661/661 (100 %) | 0 diff (100 %id) |
yk427e6.5 | | .a | 7 to 757 | 26 to 775 | | | 750/751 (99 %) | 1 diff (99.9 %id) |
yk703c1.3 | whole animal | .a | 917 to 1755 | 839 to 1 | | | 839/872 (96 %) | 0 diff (100 %id) |
yk703c1.5 | whole animal | .a | 1 to 594 | 113 to 708 | SL2 | | 596/626 (95 %) | 6 diff (99.1 %id) |
yk741f5.3 | whole animal | .a | 985 to 1763 | 780 to 1 | | | 780/780 (100 %) | 1 diff (99.9 %id) |
yk741f5.5 | whole animal | .a | 1 to 576 | 83 to 661 | SL2 | | 579/705 (82 %) | 9 diff (98.8 %id) |
GB:BJ112939 | whole animal | .a | 1 to 630 | 22 to 651 | SL2 | | 630/630 (100 %) | 0 diff (100 %id) |
yk1162b4.3 | whole animal | .a | 805 to 1763 | 959 to 1 | tiling clone, | | 959/959 (100 %) | 0 diff (100 %id) |
GB:BJ121359 | whole animal | .a | 1 to 579 | 23 to 601 | SL2 | | 579/579 (100 %) | 4 diff (99.4 %id) |
yk1275d4.3 | whole animal | .a | 863 to 1763 | 901 to 1 | | | 901/904 (99 %) | 0 diff (100 %id) |
yk1406a4.5 | | .a | 1731 to 1814 | 59 to 142 | tiling clone, AAA | | 84/84 (100 %) | 0 diff (100 %id) |
yk1506b2.3 | whole animal | .a | 847 to 1768 | 922 to 1 | | | 922/926 (99 %) | 1 diff (99.9 %id) |
yk1506b2.5 | whole animal | .a | 1 to 823 | 83 to 901 | SL2 | | 819/827 (99 %) | 7 diff (99.2 %id) |
yk1522a5.3 | whole animal | .a | 838 to 1753 | 916 to 1 | | | 916/918 (99 %) | 1 diff (99.9 %id) |
yk1522a5.5 | whole animal | .a | 1 to 195 | 80 to 276 | SL3 | | 197/641 (30 %) | 7 diff (99.0 %id) |
yk1756a10.5 | whole animal | .a | 1 to 783 | 77 to 859 | tiling clone, SL2 | | 783/783 (100 %) | 0 diff (100 %id) |
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'.
If you know more about this gene, or found errors, please share your knowledge. Thank you !