Homo sapiens gene CNIH, encoding cornichon homolog (Drosophila).
SUMMARY back to top
RefSeq annotates one representative transcript (NM included in AceView variant.b), but Homo sapiens cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 8 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 2.7 times the average gene in this release. The sequence of this gene is defined by 312 GenBank accessions from 281 cDNA clones, some from brain (seen 21 times), lung (18), breast carcinoma (14), eye (11), testis (10), breast (8), colon (8) and 103 other tissues. We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 12 distinct gt-ag introns. Transcription produces 10 different mRNAs, 8 alternatively spliced variants and 2 unspliced forms. There are 2 non overlapping alternative last exons and 5 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by presence or absence of 6 cassette exons, overlapping exons with different boundaries.
Note that mRNA .gAug10 was found in vivo, although it is a predicted target of nonsense mediated mRNA decay (NMD).
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant bAug10).
Function: There are 4 articles specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in processes (immune response, signal transduction, intracellular signaling pathway, vesicle-mediated transport). Proteins are expected to localize in various compartments (endoplasmic reticulum membrane, Golgi apparatus, Golgi membrane, integral to membrane).
Protein coding potential: 7 spliced mRNAs putatively encode good proteins, altogether 6 different isoforms (5 complete, 1 COOH complete), some containing Cornichon protein domain [Pfam], some transmembrane domains [Psort2]. The remaining 3 mRNA variants (1 spliced, 2 unspliced) appear not to encode good proteins.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 14, links to other databases and other names
Map: This gene CNIH maps on chromosome 14, at 14q22.2 according to Entrez Gene. In AceView, it covers 17.91 kb, from 54908173 to 54890259 (NCBI 37, August 2010), on the reverse strand.
Links to: the SNP view, gene overviews from Entrez Gene 10175, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as CNIH, UNQ155/PRO181, CNIL, CNIH1, TGAM77 or MGC117156, LOC10175. It has been described as protein cornichon homolog, cornichon-like, T-cell growth-associated molecule 77.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Cnih (e=3 10-62).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene 5N661 (e=2 10-33).
The closest A.thaliana genes, according to BlastP, are the AceView genes AT1G12340 (e=2 10-07), AT1G12390 (e=9 10-07), AT3G12180 (e=10-06), AT1G62880andAT1G62890 (e=2 10-06)
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the Flash version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
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.
Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
Downstream sequence
aAug10 837 bp 181 aa 291 bp 2kb 13868 bp 1kb
bAug10 1448 bp 144 aa 128 bp 885 bp 168 bp 2kb including Promoter 14527 bp 1kb
cAug10 684 bp 136 aa 15 bp 258 bp 2kb including Promoter 13750 bp 1kb
dAug10 568 bp 136 aa 58 bp 99 bp 2kb including Promoter 11228 bp 1kb
eAug10 778 bp 128 aa 23 bp 389 bp 2kb probably including promoter 13926 bp 1kb
fAug10 4627 bp 96 aa 63 bp 4273 bp 2kb including Promoter 17850 bp 1kb
gAug10 882 bp 69 aa 50 bp 670 bp 2kb probably including promoter 14074 bp 1kb
hAug10-unspliced 1050 bp 36 aa 762 bp 177 bp 2kb 1050 bp 1kb
iAug10 780 bp 80 aa 321 bp 216 bp 2kb probably including promoter 13743 bp 1kb
jAug10-unspliced 280 bp 57 aa 29 bp 77 bp 2kb 280 bp 1kb

Gene neighbors and Navigator on chromosome 14q22.2 back to top
ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications        
Annotated mRNA diagrams back to top
Bibliography:               4 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h-u, .i, .j-u 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 !