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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Homo sapiens gene FFAR2, encoding free fatty acid receptor 2.
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. 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.
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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 islets of langerhans (seen 4 times), pancreas (4), lung (2), alveolar macrophage (once), ascites (once), g-protein coupled receptors obtained bypcr-directed strategy (once), stomach (once).
23 cDNA clones support the 2 variants of gene FFAR2
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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. |
Clone encodes complete protein (with AA variation) |
Features |
Anomalies detected by AceView |
Accession match over (% length) |
Base differences relative to genome (% identity) |
AX810701 | | .a | 1 to 1329 | 1 to 1329 | S33X V173X L207X I216X V286X | tiling clone, | | 1329/1329 (100 %) | 0 diff (100 %id) |
AB378083 | | .a | 81 to 1586 | 1 to 1508 | | | | 1508/1508 (100 %) | 4 diff (99.8 %id) |
NM_005306.2 | | .a | 81 to 2131 | 1 to 2051 | | RefSeq, AAA | Possibly primed on the genome, locally A rich (23/23 A in genome downstream of last aligned base) | 2051/2051 (100 %) | 0 diff (100 %id) |
CK819813 | Islets of Langerhans, Pancreas | .a | 996 to 1605 | 610 to 1 | | tiling clone, | | 610/610 (100 %) | 0 diff (100 %id) |
BF106231 | lung | .a | 1007 to 1592 | 1 to 586 | | | | 586/586 (100 %) | 4 diff (99.4 %id) |
BM141718 | Islets of Langerhans, Pancreas | .a | 1097 to 1605 | 509 to 1 | | | | 509/509 (100 %) | 4 diff (99.3 %id) |
CA309917 | Alveolar Macrophage, lung | .a | 1556 to 2131 | 594 to 19 | | tiling clone, AAA | Possibly primed on the genome, locally A rich (23/23 A in genome downstream of last aligned base) | 576/576 (100 %) | 0 diff (100 %id) |
BM791838 | Ascites, stomach | .a | 1734 to 2129 | 1 to 396 | | AAA | Possibly primed on the genome, locally A rich (23/23 A in genome downstream of last aligned base) | 396/396 (100 %) | 2 diff (99.5 %id) |
AW015185 | | .a | 1877 to 2131 | 272 to 18 | | AAA | Possibly primed on the genome, locally A rich (23/23 A in genome downstream of last aligned base) | 255/255 (100 %) | 0 diff (100 %id) |
CK819814 | Islets of Langerhans, Pancreas | .b-u | 1 to 118 | 1 to 119 | | tiling clone, | | 119/119 (100 %) | 1 diff (99.2 %id) |
BM141985 | Islets of Langerhans, Pancreas | .b-u | 17 to 569 | 1 to 553 | | tiling clone, | | 553/553 (100 %) | 0 diff (100 %id) |
CN841942 | mixed | .b-u | 111 to 566 | 3 to 462 | | fully sequenced, | | 460/462 (99 %) | 5 diff (99.0 %id) |
CN835438 | mixed | .b-u | 111 to 853 | 3 to 753 | | fully sequenced, | | 751/753 (99 %) | 9 diff (98.9 %id) |
CN833525 | mixed | .b-u | 111 to 368 | 3 to 277 | | fully sequenced, | | 275/277 (99 %) | 5 diff (98.2 %id) |
CN841411 | mixed | .b-u | 111 to 311 | 3 to 212 | | fully sequenced, | | 210/212 (99 %) | 5 diff (97.7 %id) |
BC096198 | PCR rescued clones | .b-u | 117 to 1109 | 1 to 993 | exact | tiling clone, | | 993/993 (100 %) | 0 diff (100 %id) |
BC096199 | PCR rescued clones | .b-u | 117 to 1109 | 1 to 993 | exact | | | 993/993 (100 %) | 0 diff (100 %id) |
BC096201 | PCR rescued clones | .b-u | 117 to 1109 | 1 to 993 | T227M | | | 993/993 (100 %) | 1 diff (99.9 %id) |
CN839425 | mixed | .b-u | 117 to 846 | 9 to 747 | | | | 739/863 (85 %) | 10 diff (98.9 %id) |
CN843465 | mixed | .b-u | 117 to 897 | 9 to 797 | | | | 789/841 (93 %) | 15 diff (98.3 %id) |
BC096200 | PCR rescued clones | .b-u | 117 to 1108 | 1 to 992 | | | | 992/992 (100 %) | 0 diff (100 %id) |
BC095535 | G-protein coupled receptors obtained byPCR-directed strategy | .b-u | 120 to 1108 | 1 to 989 | | | | 989/989 (100 %) | 0 diff (100 %id) |
CN843466 | mixed | .b-u | 231 to 1100 | 879 to 2 | | | | 878/900 (97 %) | 0 diff (100 %id) |
CN841363 | mixed | .b-u | 281 to 1107 | 837 to 1 | | fully sequenced, | | 837/837 (100 %) | 8 diff (99.1 %id) |
CN833548 | mixed | .b-u | 338 to 1085 | 752 to 1 | | fully sequenced, | | 752/752 (100 %) | 7 diff (99.1 %id) |
CN842006 | mixed | .b-u | 536 to 1102 | 567 to 1 | | fully sequenced, | | 567/567 (100 %) | 1 diff (99.9 %id) |
CN835485 | mixed | .b-u | 823 to 1116 | 354 to 55 | | fully sequenced, | | 300/354 (84 %) | 5 diff (98.6 %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'.
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