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 elegans essential gene cogc-4, encoding conserved Oligomeric Golgi Component.
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 23 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 27 times), all tissues (2).
Libraries: Kohara embryonic lambda gt11 library: yk402e5, yk399e12, yk184c5, yk667a5, yk83f8, yk619e7;
early embryo, Stratagene library [PMID1302005]: CEESQ78;
Kohara Sugano L1 larvae cap-selected library: yk1069c4, yk1145d2;
Kohara Sugano L2 larvae cap-selected library: yk1567d6, yk1398a8, yk800c5, yk816b11;
Kohara mixed stage library, from him-8 strain, containing 15-30% males: yk73d3, yk145a3, yk555g2, yk205b1, yk92f2, yk22a2;
Marc Vidal ORFeome library [Nat Genet. 2003 May;34(1):35-41]: OST_10113D5, OST_10113C8.
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 27%, L1 or L2 larvae 23%, L3 to adult 50%.
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.
23 cDNA clones support the 3 variants of gene cogc-4
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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) |
CEESQ78F | | .a | 2459 to 2797 | 339 to 1 | tiling clone, | Submitted on the opposite strand | 339/339 (100 %) | 0 diff (100 %id) |
OSTF_10113C8 | whole animal | .a | 1989 to 2100 | 222 to 111 | fully sequenced, | Submitted on the opposite strand, submitted on the opposite strand (both the F and R reads are the opposite of what they should be: F is 3' and R is 5', so the insert is in the opposite direction relative to the vector and the clone should not produce any recognizable protein) | 112/112 (100 %) | 0 diff (100 %id) |
OSTR_10113C8 | whole animal | .a | 1842 to 2100 | 123 to 381 | fully sequenced, | Submitted on the opposite strand, submitted on the opposite strand (both the F and R reads are the opposite of what they should be: F is 3' and R is 5', so the insert is in the opposite direction relative to the vector and the clone should not produce any recognizable protein) | 259/259 (100 %) | 1 diff (99.7 %id) |
OSTF_10113D5 | whole animal | .a | 6 to 235 | 110 to 339 | fully sequenced, | | 230/230 (100 %) | 20 diff (91.4 %id) |
OSTR_10113D5 | whole animal | .a | 42 to 237 | 319 to 124 | fully sequenced, | | 196/196 (100 %) | 0 diff (100 %id) |
OSTF_1030025C04 | all tissues | .c | 2 to 384 | 78 to 461 | tiling clone, fully sequenced, | | 384/384 (100 %) | 0 diff (100 %id) |
OSTR_1030025C04 | all tissues | .c | 354 to 956 | 706 to 95 | tiling clone, fully sequenced, | | 612/612 (100 %) | 1 diff (99.9 %id) |
yk22a2.3 | whole animal | .a | 2221 to 2794 | 601 to 25 | | | 577/685 (84 %) | 7 diff (99.0 %id) |
yk22a2.5 | whole animal | .a | 230 to 710 | 20 to 500 | | | 481/554 (86 %) | 1 diff (99.9 %id) |
yk73d3.5 | whole animal | .a | 463 to 981 | 16 to 534 | | | 519/519 (100 %) | 0 diff (100 %id) |
yk83f8.3 | | .a | 2398 to 2784 | 474 to 88 | | | 387/581 (66 %) | 0 diff (100 %id) |
yk83f8.5 | | .a | 329 to 723 | 15 to 409 | | | 395/502 (78 %) | 5 diff (99.1 %id) |
yk92f2.3 | whole animal | .a | 2356 to 2790 | 453 to 22 | fully sequenced, | | 432/453 (95 %) | 4 diff (99.2 %id) |
yk92f2.5 | whole animal | .a | 2027 to 2386 | 31 to 394 | fully sequenced, | | 364/364 (100 %) | 1 diff (99.8 %id) |
yk145a3.3 | whole animal | .a | 2472 to 2786 | 317 to 3 | | | 315/648 (48 %) | 8 diff (98.8 %id) |
yk145a3.5 | whole animal | .a | 698 to 1522 | 25 to 851 | | | 827/926 (89 %) | 6 diff (99.4 %id) |
yk184c5.3 | | .a | 2368 to 2687 | 427 to 106 | | | 322/725 (44 %) | 17 diff (97.7 %id) |
yk184c5.5 | | .a | 250 to 765 | 17 to 532 | | | 516/516 (100 %) | 0 diff (100 %id) |
yk205b1.3 | whole animal | .a | 2238 to 2790 | 553 to 1 | | | 553/778 (71 %) | 5 diff (99.4 %id) |
yk205b1.5 | whole animal | .a | 1435 to 2105 | 32 to 700 | | | 669/698 (95 %) | 1 diff (99.9 %id) |
yk399e12.5 | | .a | 6 to 583 | 22 to 600 | | | 579/784 (73 %) | 1 diff (99.9 %id) |
yk400b1.3 | | .b | 599 to 1115 | 517 to 1 | tiling clone, fully sequenced, | | 517/517 (100 %) | 0 diff (100 %id) |
yk400b1.5 | | .b | 1 to 616 | 25 to 639 | tiling clone, fully sequenced, | | 615/615 (100 %) | 3 diff (99.6 %id) |
yk402e5.3 | | .a | 2214 to 2774 | 570 to 10 | | | 561/570 (98 %) | 4 diff (99.3 %id) |
yk402e5.5 | | .a | 1 to 633 | 22 to 654 | | | 635/774 (82 %) | 4 diff (99.5 %id) |
yk555g2.3 | whole animal | .a | 2150 to 2786 | 636 to 1 | | | 636/733 (86 %) | 2 diff (99.8 %id) |
yk555g2.5 | whole animal | .a | 1430 to 2123 | 25 to 718 | | | 694/695 (99 %) | 1 diff (99.9 %id) |
GB:AV181377 | | .a | 2443 to 2733 | 291 to 1 | | | 291/300 (97 %) | 9 diff (97.0 %id) |
yk619e7.5 | | .a | 360 to 1030 | 20 to 690 | | | 671/721 (93 %) | 1 diff (99.9 %id) |
yk667a5.3 | | .a | 2158 to 2784 | 639 to 11 | | | 629/639 (98 %) | 5 diff (99.3 %id) |
yk667a5.5 | | .a | 298 to 800 | 18 to 520 | | | 503/660 (76 %) | 1 diff (99.9 %id) |
yk800c5.3 | whole animal | .a | 1850 to 2795 | 946 to 1 | tiling clone, | | 946/947 (99 %) | 0 diff (100 %id) |
yk800c5.5 | whole animal | .a | 1 to 861 | 87 to 948 | SL8 | | 862/863 (99 %) | 2 diff (99.8 %id) |
yk816b11.3 | whole animal | .a | 1875 to 2795 | 920 to 1 | | | 920/920 (100 %) | 2 diff (99.8 %id) |
yk816b11.5 | whole animal | .a | 1 to 837 | 88 to 924 | tiling clone, SL3 | | 837/838 (99 %) | 1 diff (99.9 %id) |
yk1069c4.3 | whole animal | .a | 1870 to 2794 | 924 to 2 | | | 923/928 (99 %) | 12 diff (98.8 %id) |
yk1069c4.5 | whole animal | .a | 1 to 749 | 86 to 835 | SL2 | | 750/750 (100 %) | 3 diff (99.6 %id) |
yk1145d2.3 | whole animal | .a | 1533 to 2795 | 937 to 1 | fully sequenced, | Suspected internal deletion | 937/937 (100 %) | 6 diff (99.4 %id) |
yk1145d2.5 | whole animal | .a | 775 to 1563 | 66 to 860 | tiling clone, fully sequenced, | Suspected internal deletion | 795/795 (100 %) | 3 diff (99.7 %id) |
yk1398a8.3 | whole animal | .a | 1916 to 2785 | 870 to 1 | | | 870/871 (99 %) | 4 diff (99.6 %id) |
yk1398a8.5 | whole animal | .a | 1 to 850 | 81 to 929 | SL9 | | 849/849 (100 %) | 0 diff (100 %id) |
yk1567d6.3 | whole animal | .a | 770 to 2770 | 917 to 1 | fully sequenced, | Suspected internal deletion | 917/917 (100 %) | 7 diff (99.3 %id) |
yk1567d6.5 | whole animal | .a | 1 to 800 | 76 to 875 | fully sequenced, SL4 | Suspected internal deletion | 800/800 (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 !