AceView offers a comprehensive annotation of human, mouse and nematode genes
reconstructed by co-alignment and clustering of all publicly available
mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable
up-to-date resource on the genes, their functions, alternative variants,
expression, regulation and interactions, in the hope to stimulate
further validating experiments at the bench
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Caenorhabditis eleganswith phenotype 3H390.
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 32 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 47 times), all tissues (2).
Libraries: Kohara Sugano L1 larvae cap-selected library: yk1306b5;
Kohara mixed stage library, from him-8 strain, containing 15-30% males: yk234b5, yk408h9;
Marc Vidal ORFeome library [Nat Genet. 2003 May;34(1):35-41]: OST_10053F2.
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 8%, L1 or L2 larvae 44%, L3 to adult 48%.
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.
32 cDNA clones support the 5 variants of gene 3H390
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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) |
EX1776808_3 | | .b | 514 to 1017 | 119 to 626 | AAA | | 508/600 (84 %) | 12 diff (98.0 %id) |
EX2712556 | | .b | 1412 to 2025 | 84 to 703 | | | 620/710 (87 %) | 21 diff (97.1 %id) |
EX2718740 | | .b | 1343 to 2030 | 101 to 787 | | | 687/693 (99 %) | 41 diff (94.1 %id) |
CEESX28R | | .d | 1 to 353 | 20 to 378 | SL1 | | 359/359 (100 %) | 10 diff (97.3 %id) |
CEMSA16F | | .b | 1421 to 1853 | 435 to 1 | | Submitted on the opposite strand | 435/439 (99 %) | 5 diff (98.9 %id) |
CEMSA16R | | .b | 662 to 886 | 1 to 226 | | Submitted on the opposite strand | 226/287 (78 %) | 3 diff (99.0 %id) |
OSTF053F2_2 | whole animal | .a | 33 to 632 | 109 to 708 | | | 600/601 (99 %) | 15 diff (97.6 %id) |
OSTR053F2_2 | whole animal | .a | 1262 to 1830 | 693 to 125 | | | 569/569 (100 %) | 0 diff (100 %id) |
OSTF_1030002B07 | all tissues | .b | 13 to 789 | 94 to 882 | | | 789/810 (97 %) | 17 diff (98.0 %id) |
OSTR_1030002B07 | all tissues | .b | 895 to 1648 | 873 to 101 | | | 773/814 (94 %) | 25 diff (97.0 %id) |
yk218e3.3 | whole animal | .b | 1804 to 2116 | 313 to 1 | tiling clone, fully sequenced, | | 313/313 (100 %) | 0 diff (100 %id) |
yk218e3.5 | whole animal | .b | 1548 to 2094 | 20 to 566 | fully sequenced, | | 547/547 (100 %) | 4 diff (99.3 %id) |
yk234b5.3 | whole animal | .a | 1473 to 2293 | 821 to 1 | fully sequenced, | | 821/821 (100 %) | 2 diff (99.8 %id) |
yk234b5.5 | whole animal | .a | 846 to 1503 | 27 to 684 | fully sequenced, | | 658/658 (100 %) | 0 diff (100 %id) |
yk408h9.3 | whole animal | .a | 1752 to 2171 | 553 to 134 | | | 420/611 (68 %) | 0 diff (100 %id) |
yk408h9.5 | whole animal | .a | 1 to 640 | 26 to 666 | tiling clone, | | 641/708 (90 %) | 3 diff (99.6 %id) |
yk477f6.3 | | .b | 1456 to 2110 | 655 to 1 | | | 655/655 (100 %) | 0 diff (100 %id) |
yk477f6.5 | | .b | 4 to 739 | 30 to 765 | | | 736/737 (99 %) | 1 diff (99.9 %id) |
yk730a10.3 | whole animal | .b | 943 to 1839 | 910 to 1 | | | 910/918 (99 %) | 20 diff (97.9 %id) |
yk730a10.5 | whole animal | .b | 1 to 828 | 93 to 921 | SL1 | | 829/830 (99 %) | 3 diff (99.7 %id) |
yk758a12.3 | whole animal | .b | 1304 to 1871 | 567 to 1 | | | 567/571 (99 %) | 1 diff (99.9 %id) |
yk758a12.5 | whole animal | .b | 107 to 998 | 63 to 954 | | | 892/893 (99 %) | 1 diff (99.9 %id) |
yk861f9.3 | whole animal | .b | 959 to 1837 | 880 to 1 | | | 880/889 (98 %) | 7 diff (99.3 %id) |
yk861f9.5 | whole animal | .b | 1 to 848 | 82 to 930 | SL1 | | 849/850 (99 %) | 10 diff (98.9 %id) |
yk876d2.3 | whole animal | .b | 905 to 1850 | 947 to 1 | | | 947/947 (100 %) | 13 diff (98.7 %id) |
yk899g11.3 | whole animal | .b | 912 to 1850 | 935 to 1 | | | 935/985 (94 %) | 17 diff (98.3 %id) |
yk899g11.5 | whole animal | .b | 1 to 851 | 86 to 943 | SL1 | | 858/860 (99 %) | 16 diff (98.2 %id) |
yk1073h2.3 | whole animal | .b | 1194 to 2109 | 916 to 3 | | | 914/918 (99 %) | 8 diff (99.2 %id) |
yk1073h2.5 | whole animal | .b | 1 to 855 | 87 to 947 | SL1 | | 861/861 (100 %) | 18 diff (98.0 %id) |
yk1084h8.3 | whole animal | .b | 954 to 1850 | 903 to 1 | | | 903/904 (99 %) | 11 diff (98.8 %id) |
yk1084h8.5 | whole animal | .b | 1 to 656 | 89 to 751 | SL1 | | 663/850 (78 %) | 18 diff (97.9 %id) |
yk1086b6.3 | whole animal | .b | 1042 to 1850 | 811 to 1 | fully sequenced, | | 811/811 (100 %) | 5 diff (99.4 %id) |
yk1086b6.5 | whole animal | .b | 220 to 1072 | 68 to 922 | fully sequenced, | | 855/855 (100 %) | 2 diff (99.8 %id) |
GB:BJ115629 | whole animal | .b | 1 to 415 | 23 to 436 | SL1 | | 414/414 (100 %) | 1 diff (99.8 %id) |
yk1193f12.3 | whole animal | .b | 888 to 1849 | 959 to 1 | | | 959/967 (99 %) | 17 diff (98.3 %id) |
yk1204e7.3 | whole animal | .b | 1175 to 2111 | 929 to 3 | | | 927/940 (98 %) | 32 diff (96.6 %id) |
GB:BJ116721 | whole animal | .b | 1 to 579 | 23 to 601 | SL1 | | 579/579 (100 %) | 0 diff (100 %id) |
yk1206e10.3 | whole animal | .b | 1174 to 2112 | 938 to 2 | | | 937/938 (99 %) | 26 diff (97.3 %id) |
yk1289b1.3 | whole animal | .b | 1188 to 2109 | 913 to 3 | | | 911/913 (99 %) | 27 diff (97.1 %id) |
yk1289b1.5 | whole animal | .b | 1 to 640 | 82 to 721 | SL1 | | 640/759 (84 %) | 5 diff (99.4 %id) |
yk1297d12.5 | whole animal | .b | 1 to 785 | 83 to 883 | SL1 | | 801/857 (93 %) | 21 diff (97.6 %id) |
yk1298d2.3 | whole animal | .b | 955 to 1833 | 878 to 1 | | | 878/878 (100 %) | 12 diff (98.7 %id) |
yk1298d2.5 | whole animal | .b | 1 to 801 | 88 to 889 | tiling clone, SL1 | | 802/802 (100 %) | 3 diff (99.7 %id) |
yk1306b5.3 | whole animal | .a | 1400 to 2294 | 895 to 1 | fully sequenced, | | 895/895 (100 %) | 12 diff (98.7 %id) |
yk1306b5.5 | whole animal | .a | 558 to 1430 | 68 to 947 | tiling clone, fully sequenced, | | 880/880 (100 %) | 13 diff (98.6 %id) |
yk1347c5.3 | whole animal | .b | 887 to 1850 | 963 to 1 | | | 963/965 (99 %) | 15 diff (98.5 %id) |
yk1347c5.5 | whole animal | .b | 1 to 823 | 86 to 905 | SL8 | | 820/821 (99 %) | 9 diff (99.0 %id) |
yk1377f8.3 | whole animal | .c | 1276 to 2217 | 938 to 1 | tiling clone, | | 938/942 (99 %) | 12 diff (98.8 %id) |
yk1377f8.5 | whole animal | .c | 1 to 827 | 80 to 909 | tiling clone, SL1 | | 830/832 (99 %) | 5 diff (99.4 %id) |
yk1398h9.3 | whole animal | .b | 1227 to 2107 | 875 to 1 | tiling clone, | | 875/875 (100 %) | 11 diff (98.8 %id) |
yk1398h9.5 | whole animal | .b | 1 to 843 | 81 to 925 | SL1 | | 845/852 (99 %) | 8 diff (99.1 %id) |
yk1440a9.3 | whole animal | .b | 908 to 1847 | 944 to 1 | | | 944/945 (99 %) | 12 diff (98.8 %id) |
yk1440a9.5 | whole animal | .b | 1 to 819 | 83 to 902 | SL1 | | 820/820 (100 %) | 5 diff (99.4 %id) |
yk1547c10.3 | whole animal | .b | 1450 to 2107 | 656 to 1 | | | 656/923 (71 %) | 14 diff (98.5 %id) |
yk1547c10.5 | whole animal | .b | 1 to 820 | 88 to 911 | SL1 | | 824/824 (100 %) | 6 diff (99.3 %id) |
yk1643c2.3 | whole animal | .b | 1002 to 1845 | 846 to 1 | fully sequenced, | | 846/846 (100 %) | 5 diff (99.5 %id) |
yk1643c2.5 | whole animal | .b | 218 to 1032 | 56 to 878 | fully sequenced, | | 823/823 (100 %) | 11 diff (98.7 %id) |
? | Gene Summary |
Gene on genome |
mRNA:.a, .b, .c, .d, .e |
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'.
If you know more about this gene, or found errors, please share your knowledge. Thank you !