Homo sapiens complex locus CNGB1, encoding cyclic nucleotide gated channel beta 1.
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SUMMARY back to top
RefSeq summary
[CNGB1] In humans, the rod photoreceptor cGMP-gated cation channel helps regulate ion flow into the rod photoreceptor outer segment in response to light-induced alteration of the levels of intracellular cGMP. This channel consists of two subunits, alpha and beta, with the protein encoded by this gene representing the beta subunit. Defects in this gene are a cause of cause of retinitis pigmentosa type 45. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq].

RefSeq annotates 2 representative transcripts (NM included in AceView variants .a and .c), 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 9 spliced variants.

AceView synopsis, each blue text links to tables and details
Note that this locus is complex: it appears to produce several proteins with no sequence overlap.
Expression: According to AceView, this gene is well expressed, 0.6 times the average gene in this release. The sequence of this gene is defined by 67 GenBank accessions from 46 cDNA clones, some from eye (seen 18 times), retina (13), eyeball (6), amygdala (5), optic nerve (4), testis (4), brain (2) and 17 other tissues. We annotate structural defects or features in 8 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 40 distinct gt-ag introns. Transcription produces 11 different mRNAs, 9 alternatively spliced variants and 2 unspliced forms. There are 4 probable alternative promotors and 5 non overlapping alternative last exons (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 4 cassette exons, overlapping exons with different boundaries, splicing versus retention of 2 introns.
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 eAug10).
Function: There are 17 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (OMIM: retinitis pigmentosa; Other sources: Retinitis pigmentosa, autosomal recessive; Retinitis pigmentosa-45), proposed to participate in pathways (Olfactory transduction, Phototransduction) and processes (transport, visual perception, ion transport, photoreceptor cell maintenance, phototransduction, response to stimulus, sensory perception of smell). Proteins are expected to have molecular functions (ligand-gated ion channel activity, cAMP binding, intracellular cAMP activated cation channel activity, nucleotide binding) and to localize in various compartments (membrane, nucleus, integral to membrane, intracellular cyclic nucleotide activated cation channel complex, membrane fraction). Putative protein interactors have been described (ABCA4, PNN, PRPH2).
Protein coding potential: 9 spliced mRNAs putatively encode good proteins, altogether 9 different isoforms (5 complete, 3 COOH complete, 1 partial), some containing domains Cyclic nucleotide-binding domain, Ion transport protein [Pfam], some transmembrane domains, a coiled coil stretch [Psort2]. The remaining 2 mRNA variants (2 unspliced; 2 partial) appear not to encode good proteins.
Isoform CNGB1.eAug10 is annotated using as Met a Kozak-compatible a..GTG. start, thereby gaining 84 amino acids N-terminal to the first AUG. Finally proteins from this gene may be modulated by acetylation; phosphorylation, as detailed at PhosphoSite.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 16, links to other databases and other names
Map: This gene CNGB1 maps on chromosome 16, at 16q13 according to Entrez Gene. In AceView, it covers 88.78 kb, from 58005020 to 57916244 (NCBI 37, August 2010), on the reverse strand.
Links to: manual annotations from OMIM_268000, KEGG_04740, KEGG_04744, PhosphoSite, the SNP view, gene overviews from Entrez Gene 1258, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC. The previous AceView annotation is here.
Other names: The gene is also known as CNGB1, CNG4, GAR1, GARP, RP45, CNCG2, CNCG4, RCNC2, RCNCb, CNCG3L, CNGB1B, RCNCbeta, LOC1258, storworbu or persnar, peesnar. It has been described as cyclic nucleotide-gated cation channel beta-1, CNG-4, CNG channel beta-1, glutamic acid-rich protein, glutamic-acid-rich protein, cyclic nucleotide-gated channel beta-1, cyclic nucleotide-gated cation channel 4, cyclic nucleotide-gated cation channel gamma, cyclic nucleotide-gated cation channel modulatory subunit, cyclic nucleotide gated channel (photoreceptor), cGMP gated 3 (gamma)-like.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene BC016201 (e=2 10-26).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene tax-2 (e=10-49), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes ATCNGC10 (e=10-12), AKT2 (e=2 10-10), ATCNGC17 (e=2 10-10), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
CNGB1 Gene expression in 15 primates, 16 tissues, from the NHPRTR project in sFPKM BAB SkeletalMuscle WholeBlood CHP Kidney Liver Lung Spleen CMC CMM Cerebellum HUM Brain Colon Heart LymphNode Ovary Testis JMI BoneMarrow MLM OWL PTM RMC RMI Pituitary SQM Thymus MST SMY RTL 0.17 2.19 0.78 0.04 0.10 0.04 0.04 0.12 0.04 0.42 0.63 0.19 0.22 0.08 0.11 0.32 0.78 0.14 0.05 0.06 0.10 0.07 0.08 0.27 0.13 0.05 0.17 0.10 0.10 0.10 0.24 0.12 1.66 0.05 0.13 0.16 0.34 0.22 2.35 0.14 0.09 0.05 0.04 0.17 0.07 0.07 0.10 0.04 0.34 0.08 0.04 0.08 0.06 1.26 0.06 0.07 0.06 0.72 0.17 0.78 0.10 0.07 0.07 0.05 0.08 0.06 0.04 0.09 0.08 0.08 0.39 0.09 0.12 0.08 0.09 0.09 0.08 0.07 1.45 0.04 0.05 0.06 0.07 0.11 0.08 0.06 0.29 0.04 0.07 0.07 0.14 0.14 4.10 0.14 0.18 1.35 0.10 0.26 0.24 0.06 0.06 0.09 0.08 0.10 0.13 0.14 0.39 Expression quantiles None Weak 1 2 3 4 5 6 7 8 10 20 This gene All genes log2 distributions 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!.
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          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene CNGB1 5' 3' encoded on minus strand of chromosome 16 from 58,005,020 to 57,916,244 43 77 71 57 54 57 53 53 57 61 23 26 23 10943 8134 a [NM] 43 77 71 57 54 57 53 53 57 61 23 26 23 10943 8134 b 43 77 71 57 54 57 53 53 57 61 150 c [NM] 294 h k-u 1271 d 43 77 71 g e j-u 77 71 57 54 57 53 53 f 3 i 10kb 0 57 bp exon 3765 bp [gt-ag] intron 10 GenBank accessions 33 RNA-seq supporting reads 1 Brain 32 Neuroblastoma (also 7 Primates bodymap) 167 bp exon 167 bp exon 2583 bp [gt-ag] intron 11 GenBank accessions 66 RNA-seq supporting reads 1 UHR pooled cells 61 Neuroblastoma 4 Other (also 44 Primates bodymap) 58 bp exon 284 bp [gt-ag] intron 11 GenBank accessions 60 RNA-seq supporting reads 3 Brain 55 Neuroblastoma 2 Other (also 28 Primates bodymap) 73 bp exon 1065 bp [gt-ag] intron 9 GenBank accessions 48 RNA-seq supporting reads 1 UHR pooled cells 2 Brain 45 Neuroblastoma (also 16 Primates bodymap) 91 bp exon 101 bp [gt-ag] intron 9 GenBank accessions 45 RNA-seq supporting reads 2 Brain 3 Blood 40 Neuroblastoma (also 25 Primates bodymap) 31 bp exon 231 bp [gt-ag] intron 9 GenBank accessions 48 RNA-seq supporting reads 3 Brain 45 Neuroblastoma (also 20 Primates bodymap) 46 bp exon 1649 bp [gt-ag] intron 8 GenBank accessions 45 RNA-seq supporting reads 6 Brain 39 Neuroblastoma 76 bp exon 309 bp [gt-ag] intron 8 GenBank accessions 45 RNA-seq supporting reads 1 Brain 44 Neuroblastoma (also 14 Primates bodymap) 49 bp exon 416 bp [gt-ag] intron 5 GenBank accessions 37 RNA-seq supporting reads 1 UHR pooled cells 36 Neuroblastoma (also 29 Primates bodymap) 178 bp exon 1402 bp [gt-ag] intron 7 GenBank accessions 50 RNA-seq supporting reads 2 Brain 48 Neuroblastoma (also 27 Primates bodymap) 76 bp exon 1032 bp [gt-ag] intron 9 GenBank accessions 52 RNA-seq supporting reads 52 Neuroblastoma (also 32 Primates bodymap) 37 bp exon 6800 bp [gt-ag] intron 5 GenBank accessions 18 RNA-seq supporting reads 18 Neuroblastoma (also 14 Primates bodymap) 160 bp exon 941 bp [gt-ag] intron 5 GenBank accessions 21 RNA-seq supporting reads 1 Brain 20 Neuroblastoma (also 14 Primates bodymap) 87 bp exon 9031 bp [gt-ag] intron 5 GenBank accessions 18 RNA-seq supporting reads 18 Neuroblastoma (also 4 Primates bodymap) 88 bp exon 641 bp [gt-ag] intron 10 GenBank accessions 28690 RNA-seq supporting reads 2 UHR pooled cells 187 Brain 28472 Neuroblastoma 29 Other (also 65 Primates bodymap) 163 bp exon 7551 bp [gt-ag] intron 5 GenBank accessions 10938 RNA-seq supporting reads 4 Brain 10933 Neuroblastoma 1 Other (also 1 Primates bodymap) 163 bp exon 8335 bp [gt-ag] intron 5 GenBank accessions 33416 RNA-seq supporting reads 11 UHR pooled cells 246 Brain 33095 Neuroblastoma 64 Other (also 111 Primates bodymap) 108 bp exon 2728 bp [gt-ag] intron 4 GenBank accessions 8130 RNA-seq supporting reads 2 UHR pooled cells 108 Brain 7997 Neuroblastoma 23 Other (also 36 Primates bodymap) 158 bp exon 1132 bp [gt-ag] intron 4 GenBank accessions 30440 RNA-seq supporting reads 9 UHR pooled cells 260 Brain 30122 Neuroblastoma 49 Other (also 105 Primates bodymap) 156 bp exon 1622 bp [gt-ag] intron 4 GenBank accessions 34467 RNA-seq supporting reads 14 UHR pooled cells 291 Brain 34097 Neuroblastoma 65 Other (also 83 Primates bodymap) 209 bp exon 1088 bp [gt-ag] intron 5 GenBank accessions 33710 RNA-seq supporting reads 3 UHR pooled cells 268 Brain 33366 Neuroblastoma 73 Other (also 121 Primates bodymap) 51 bp exon 793 bp [gt-ag] intron 7 GenBank accessions 25527 RNA-seq supporting reads 39 UHR pooled cells 270 Brain 1 Blood 25161 Neuroblastoma 56 Other (also 98 Primates bodymap) 87 bp exon 2254 bp [gt-ag] intron 7 GenBank accessions 30585 RNA-seq supporting reads 78 UHR pooled cells 352 Brain 30103 Neuroblastoma 52 Other (also 74 Primates bodymap) 65 bp exon 1054 bp [gt-ag] intron 7 GenBank accessions 47801 RNA-seq supporting reads 123 UHR pooled cells 392 Brain 47203 Neuroblastoma 83 Other (also 98 Primates bodymap) 123 bp exon 6877 bp [gt-ag] intron 8 GenBank accessions 32802 RNA-seq supporting reads 118 UHR pooled cells 290 Brain 1 Blood 32343 Neuroblastoma 50 Other (also 48 Primates bodymap) 142 bp exon 752 bp [gt-ag] intron 9 GenBank accessions 38338 RNA-seq supporting reads 92 UHR pooled cells 306 Brain 37853 Neuroblastoma 87 Other (also 38 Primates bodymap) 160 bp exon 2196 bp [gt-ag] intron 10 GenBank accessions 39077 RNA-seq supporting reads 147 UHR pooled cells 311 Brain 1 Blood 38532 Neuroblastoma 86 Other (also 36 Primates bodymap) 98 bp exon 92 bp [gt-ag] intron 11 GenBank accessions 55721 RNA-seq supporting reads 249 UHR pooled cells 446 Brain 1 Blood 54924 Neuroblastoma 101 Other (also 70 Primates bodymap) 84 bp exon 3437 bp [gt-ag] intron 13 GenBank accessions 58770 RNA-seq supporting reads 278 UHR pooled cells 493 Brain 57890 Neuroblastoma 109 Other (also 82 Primates bodymap) 119 bp exon 252 bp [gt-ag] intron 13 GenBank accessions 44449 RNA-seq supporting reads 177 UHR pooled cells 296 Brain 43868 Neuroblastoma 108 Other (also 123 Primates bodymap) 147 bp exon 9322 bp [gt-ag] intron 8 GenBank accessions 58965 RNA-seq supporting reads 211 UHR pooled cells 463 Brain 2 Blood 58159 Neuroblastoma 130 Other (also 102 Primates bodymap) 220 bp exon 3397 bp [gt-ag] intron 8 GenBank accessions 46731 RNA-seq supporting reads 148 UHR pooled cells 403 Brain 46126 Neuroblastoma 54 Other (also 47 Primates bodymap) 2118 bp exon 23 accessions, NM_001297.4 some from eye (seen 8 times) retina (6), fetal eyes lens, eye anterior segment optic nerve, retina, retina foveal and macular RPE andchoroid (2), amygdala (once) brain (once) 2118 bp exon 33 bp exon 3765 bp [gt-ag] intron 10 GenBank accessions 33 RNA-seq supporting reads 1 Brain 32 Neuroblastoma (also 7 Primates bodymap) 167 bp exon 167 bp exon 2583 bp [gt-ag] intron 11 GenBank accessions 66 RNA-seq supporting reads 1 UHR pooled cells 61 Neuroblastoma 4 Other (also 44 Primates bodymap) 58 bp exon 284 bp [gt-ag] intron 11 GenBank accessions 60 RNA-seq supporting reads 3 Brain 55 Neuroblastoma 2 Other (also 28 Primates bodymap) 73 bp exon 1065 bp [gt-ag] intron 9 GenBank accessions 48 RNA-seq supporting reads 1 UHR pooled cells 2 Brain 45 Neuroblastoma (also 16 Primates bodymap) 91 bp exon 101 bp [gt-ag] intron 9 GenBank accessions 45 RNA-seq supporting reads 2 Brain 3 Blood 40 Neuroblastoma (also 25 Primates bodymap) 31 bp exon 231 bp [gt-ag] intron 9 GenBank accessions 48 RNA-seq supporting reads 3 Brain 45 Neuroblastoma (also 20 Primates bodymap) 46 bp exon 1649 bp [gt-ag] intron 8 GenBank accessions 45 RNA-seq supporting reads 6 Brain 39 Neuroblastoma 76 bp exon 309 bp [gt-ag] intron 8 GenBank accessions 45 RNA-seq supporting reads 1 Brain 44 Neuroblastoma (also 14 Primates bodymap) 31 bp exon 434 bp [gt-ag] intron 2 GenBank accessions 15 RNA-seq supporting reads 1 Brain 14 Neuroblastoma 178 bp exon 1402 bp [gt-ag] intron 7 GenBank accessions 50 RNA-seq supporting reads 2 Brain 48 Neuroblastoma (also 27 Primates bodymap) 76 bp exon 1032 bp [gt-ag] intron 9 GenBank accessions 52 RNA-seq supporting reads 52 Neuroblastoma (also 32 Primates bodymap) 37 bp exon 6800 bp [gt-ag] intron 5 GenBank accessions 18 RNA-seq supporting reads 18 Neuroblastoma (also 14 Primates bodymap) 160 bp exon 941 bp [gt-ag] intron 5 GenBank accessions 21 RNA-seq supporting reads 1 Brain 20 Neuroblastoma (also 14 Primates bodymap) 87 bp exon 9031 bp [gt-ag] intron 5 GenBank accessions 18 RNA-seq supporting reads 18 Neuroblastoma (also 4 Primates bodymap) 88 bp exon 641 bp [gt-ag] intron 10 GenBank accessions 28690 RNA-seq supporting reads 2 UHR pooled cells 187 Brain 28472 Neuroblastoma 29 Other (also 65 Primates bodymap) 163 bp exon 7551 bp [gt-ag] intron 5 GenBank accessions 10938 RNA-seq supporting reads 4 Brain 10933 Neuroblastoma 1 Other (also 1 Primates bodymap) 163 bp exon 8335 bp [gt-ag] intron 5 GenBank accessions 33416 RNA-seq supporting reads 11 UHR pooled cells 246 Brain 33095 Neuroblastoma 64 Other (also 111 Primates bodymap) 108 bp exon 2728 bp [gt-ag] intron 4 GenBank accessions 8130 RNA-seq supporting reads 2 UHR pooled cells 108 Brain 7997 Neuroblastoma 23 Other (also 36 Primates bodymap) 158 bp exon 1132 bp [gt-ag] intron 4 GenBank accessions 30440 RNA-seq supporting reads 9 UHR pooled cells 260 Brain 30122 Neuroblastoma 49 Other (also 105 Primates bodymap) 156 bp exon 1622 bp [gt-ag] intron 4 GenBank accessions 34467 RNA-seq supporting reads 14 UHR pooled cells 291 Brain 34097 Neuroblastoma 65 Other (also 83 Primates bodymap) 209 bp exon 1088 bp [gt-ag] intron 5 GenBank accessions 33710 RNA-seq supporting reads 3 UHR pooled cells 268 Brain 33366 Neuroblastoma 73 Other (also 121 Primates bodymap) 51 bp exon 793 bp [gt-ag] intron 7 GenBank accessions 25527 RNA-seq supporting reads 39 UHR pooled cells 270 Brain 1 Blood 25161 Neuroblastoma 56 Other (also 98 Primates bodymap) 87 bp exon 2254 bp [gt-ag] intron 7 GenBank accessions 30585 RNA-seq supporting reads 78 UHR pooled cells 352 Brain 30103 Neuroblastoma 52 Other (also 74 Primates bodymap) 65 bp exon 1054 bp [gt-ag] intron 7 GenBank accessions 47801 RNA-seq supporting reads 123 UHR pooled cells 392 Brain 47203 Neuroblastoma 83 Other (also 98 Primates bodymap) 123 bp exon 6877 bp [gt-ag] intron 8 GenBank accessions 32802 RNA-seq supporting reads 118 UHR pooled cells 290 Brain 1 Blood 32343 Neuroblastoma 50 Other (also 48 Primates bodymap) 142 bp exon 752 bp [gt-ag] intron 9 GenBank accessions 38338 RNA-seq supporting reads 92 UHR pooled cells 306 Brain 37853 Neuroblastoma 87 Other (also 38 Primates bodymap) 160 bp exon 2196 bp [gt-ag] intron 10 GenBank accessions 39077 RNA-seq supporting reads 147 UHR pooled cells 311 Brain 1 Blood 38532 Neuroblastoma 86 Other (also 36 Primates bodymap) 98 bp exon 92 bp [gt-ag] intron 11 GenBank accessions 55721 RNA-seq supporting reads 249 UHR pooled cells 446 Brain 1 Blood 54924 Neuroblastoma 101 Other (also 70 Primates bodymap) 84 bp exon 3437 bp [gt-ag] intron 13 GenBank accessions 58770 RNA-seq supporting reads 278 UHR pooled cells 493 Brain 57890 Neuroblastoma 109 Other (also 82 Primates bodymap) 119 bp exon 252 bp [gt-ag] intron 13 GenBank accessions 44449 RNA-seq supporting reads 177 UHR pooled cells 296 Brain 43868 Neuroblastoma 108 Other (also 123 Primates bodymap) 147 bp exon 9322 bp [gt-ag] intron 8 GenBank accessions 58965 RNA-seq supporting reads 211 UHR pooled cells 463 Brain 2 Blood 58159 Neuroblastoma 130 Other (also 102 Primates bodymap) 220 bp exon 3397 bp [gt-ag] intron 8 GenBank accessions 46731 RNA-seq supporting reads 148 UHR pooled cells 403 Brain 46126 Neuroblastoma 54 Other (also 47 Primates bodymap) 864 bp exon 2 accessions 864 bp exon 57 bp exon 3765 bp [gt-ag] intron 10 GenBank accessions 33 RNA-seq supporting reads 1 Brain 32 Neuroblastoma (also 7 Primates bodymap) 167 bp exon 167 bp exon 2583 bp [gt-ag] intron 11 GenBank accessions 66 RNA-seq supporting reads 1 UHR pooled cells 61 Neuroblastoma 4 Other (also 44 Primates bodymap) 58 bp exon 284 bp [gt-ag] intron 11 GenBank accessions 60 RNA-seq supporting reads 3 Brain 55 Neuroblastoma 2 Other (also 28 Primates bodymap) 73 bp exon 1065 bp [gt-ag] intron 9 GenBank accessions 48 RNA-seq supporting reads 1 UHR pooled cells 2 Brain 45 Neuroblastoma (also 16 Primates bodymap) 91 bp exon 101 bp [gt-ag] intron 9 GenBank accessions 45 RNA-seq supporting reads 2 Brain 3 Blood 40 Neuroblastoma (also 25 Primates bodymap) 31 bp exon 231 bp [gt-ag] intron 9 GenBank accessions 48 RNA-seq supporting reads 3 Brain 45 Neuroblastoma (also 20 Primates bodymap) 46 bp exon 1649 bp [gt-ag] intron 8 GenBank accessions 45 RNA-seq supporting reads 6 Brain 39 Neuroblastoma 76 bp exon 309 bp [gt-ag] intron 8 GenBank accessions 45 RNA-seq supporting reads 1 Brain 44 Neuroblastoma (also 14 Primates bodymap) 49 bp exon 416 bp [gt-ag] intron 5 GenBank accessions 37 RNA-seq supporting reads 1 UHR pooled cells 36 Neuroblastoma (also 29 Primates bodymap) 178 bp exon 1402 bp [gt-ag] intron 7 GenBank accessions 50 RNA-seq supporting reads 2 Brain 48 Neuroblastoma (also 27 Primates bodymap) 76 bp exon 1032 bp [gt-ag] intron 9 GenBank accessions 52 RNA-seq supporting reads 52 Neuroblastoma (also 32 Primates bodymap) 37 bp exon 1972 bp [gt-ag] intron 7 GenBank accessions 143 RNA-seq supporting reads 1 Blood 142 Neuroblastoma (also 28 Primates bodymap) 692 bp exon 17 accessions, NM_001135639.1 some from eye (seen 5 times) eyeball (3), optic nerve (3) retina (3), eye anterior segment (once) Validated 3' end, 6 accessions 692 bp exon 120 bp exon 120 bp exon 16049 bp [gt-ag] intron 1 GenBank accession 293 RNA-seq supporting reads 293 Neuroblastoma 268 bp exon 1 accession from eye from retina 268 bp exon 193 bp exon 1 accession from liver 193 bp exon 148 bp exon 6877 bp [gt-ag] intron 8 GenBank accessions 32802 RNA-seq supporting reads 118 UHR pooled cells 290 Brain 1 Blood 32343 Neuroblastoma 50 Other (also 48 Primates bodymap) 142 bp exon 142 bp exon 752 bp [gt-ag] intron 9 GenBank accessions 38338 RNA-seq supporting reads 92 UHR pooled cells 306 Brain 37853 Neuroblastoma 87 Other (also 38 Primates bodymap) 160 bp exon 2196 bp [gt-ag] intron 10 GenBank accessions 39077 RNA-seq supporting reads 147 UHR pooled cells 311 Brain 1 Blood 38532 Neuroblastoma 86 Other (also 36 Primates bodymap) 98 bp exon 92 bp [gt-ag] intron 11 GenBank accessions 55721 RNA-seq supporting reads 249 UHR pooled cells 446 Brain 1 Blood 54924 Neuroblastoma 101 Other (also 70 Primates bodymap) 84 bp exon 3437 bp [gt-ag] intron 13 GenBank accessions 58770 RNA-seq supporting reads 278 UHR pooled cells 493 Brain 57890 Neuroblastoma 109 Other (also 82 Primates bodymap) 119 bp exon 252 bp [gt-ag] intron 13 GenBank accessions 44449 RNA-seq supporting reads 177 UHR pooled cells 296 Brain 43868 Neuroblastoma 108 Other (also 123 Primates bodymap) 147 bp exon 12939 bp [gt-ag] intron 3 GenBank accessions 1268 RNA-seq supporting reads 5 UHR pooled cells 14 Brain 1244 Neuroblastoma 5 Other 658 bp exon 4 accessions, some from amygdala (seen 2 times) placenta (once) capped 5' end, 1 accession 658 bp exon 50 bp exon 50 bp exon 3765 bp [gt-ag] intron 10 GenBank accessions 33 RNA-seq supporting reads 1 Brain 32 Neuroblastoma (also 7 Primates bodymap) 167 bp exon 2583 bp [gt-ag] intron 11 GenBank accessions 66 RNA-seq supporting reads 1 UHR pooled cells 61 Neuroblastoma 4 Other (also 44 Primates bodymap) 58 bp exon 284 bp [gt-ag] intron 11 GenBank accessions 60 RNA-seq supporting reads 3 Brain 55 Neuroblastoma 2 Other (also 28 Primates bodymap) 756 bp exon 2 accessions, some from eye (seen once) eyeball (once), retina (once) 756 bp exon 191 bp exon 191 bp exon 45 bp uORF 191 bp exon 6062 bp [gt-ag] intron 5 GenBank accessions 31813 RNA-seq supporting reads 189 Brain 31589 Neuroblastoma 35 Other (also 53 Primates bodymap) 88 bp exon 88 bp exon 88 bp exon 641 bp [gt-ag] intron 10 GenBank accessions 28690 RNA-seq supporting reads 2 UHR pooled cells 187 Brain 28472 Neuroblastoma 29 Other (also 65 Primates bodymap) 163 bp exon 163 bp exon 2070 bp [gt-ag] intron 5 GenBank accessions 18358 RNA-seq supporting reads 3 UHR pooled cells 219 Brain 18065 Neuroblastoma 71 Other (also 79 Primates bodymap) 268 bp exon 268 bp exon 5213 bp [gt-ag] fuzzy intron 1 GenBank accession 28423 RNA-seq supporting reads 3 UHR pooled cells 291 Brain 28036 Neuroblastoma 93 Other (also 98 Primates bodymap) 163 bp exon 163 bp exon 8335 bp [gt-ag] intron 5 GenBank accessions 33416 RNA-seq supporting reads 11 UHR pooled cells 246 Brain 33095 Neuroblastoma 64 Other (also 111 Primates bodymap) 935 bp exon 935 bp exon 5 accessions, some from amygdala (seen once) brain (once), eye (once) hippocampus (once), optic nerve (once) 935 bp exon 454 bp exon 454 bp exon 1 accession from testis 454 bp exon 225 bp exon 225 bp exon 2583 bp [gt-ag] intron 11 GenBank accessions 66 RNA-seq supporting reads 1 UHR pooled cells 61 Neuroblastoma 4 Other (also 44 Primates bodymap) 58 bp exon 284 bp [gt-ag] intron 11 GenBank accessions 60 RNA-seq supporting reads 3 Brain 55 Neuroblastoma 2 Other (also 28 Primates bodymap) 73 bp exon 1065 bp [gt-ag] intron 9 GenBank accessions 48 RNA-seq supporting reads 1 UHR pooled cells 2 Brain 45 Neuroblastoma (also 16 Primates bodymap) 91 bp exon 101 bp [gt-ag] intron 9 GenBank accessions 45 RNA-seq supporting reads 2 Brain 3 Blood 40 Neuroblastoma (also 25 Primates bodymap) 31 bp exon 231 bp [gt-ag] intron 9 GenBank accessions 48 RNA-seq supporting reads 3 Brain 45 Neuroblastoma (also 20 Primates bodymap) 46 bp exon 1649 bp [gt-ag] intron 8 GenBank accessions 45 RNA-seq supporting reads 6 Brain 39 Neuroblastoma 76 bp exon 309 bp [gt-ag] intron 8 GenBank accessions 45 RNA-seq supporting reads 1 Brain 44 Neuroblastoma (also 14 Primates bodymap) 49 bp exon 416 bp [gt-ag] intron 5 GenBank accessions 37 RNA-seq supporting reads 1 UHR pooled cells 36 Neuroblastoma (also 29 Primates bodymap) 60 bp exon 1 accession from testis 60 bp exon 15 bp exon 15 bp exon 2034 bp [gt-ag] intron 1 GenBank accession 2 RNA-seq supporting reads 2 Neuroblastoma 601 bp exon 2 accessions, some from eye (seen 2 times) retina (2) 601 bp exon 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.
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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
unit
pre-mRNA		 Downstream sequence
aAug10 5645 bp 1251 aa 65 bp 1824 bp 2kb probably including promoter 88777 bp 1kb
bAug10 4349 bp 1245 aa 41 bp 570 bp 2kb possibly including promoter 87499 bp 1kb
cAug10 1631 bp 299 aa 65 bp 666 bp 2kb probably including promoter 16440 bp 1kb
dAug10 1556 bp 357 aa 278 bp 450 bp 2kb including Promoter 28101 bp 1kb
eAug10 1808 bp 248 aa 238 bp 823 bp 42 bp 2kb possibly including promoter 24129 bp 1kb
fAug10 709 bp 214 aa 66 bp 2kb possibly including promoter 7347 bp 1kb
gAug10 1031 bp 113 aa 687 bp 2kb probably including promoter 7663 bp 1kb
hAug10 388 bp 97 aa 92 bp 2kb 16437 bp 1kb
iAug10 616 bp 95 aa 327 bp 2kb 2650 bp 1kb
jAug10-unspliced 454 bp 92 aa 173 bp 2kb 454 bp 1kb
kAug10-unspliced 193 bp 64 aa 2kb 193 bp 1kb

Gene neighbors and Navigator on chromosome 16q13 back to top
COQ9 POLR2C D C I R P GPR114 C R P GPR56 D C R P GPR97 C R P CCDC135 C R C KATNB1 C I R P R TEPP C R P C16orf57 D C I R P MMP15 C I R P R R CCDC113 C I R P GINS3 D C R P C I R P DOK4 C R CCDC102A R R D C I R P KIFC3 D C I R P CNGB1 C R P ZNF319 C I R P C16orf80 D C I R P CSNK2A2 C R P PRSS54 100kb 0 COQ9, 328 accessions, 19 variants POLR2C, 393 accessions 7 variants GPR114, 74 accessions 8 variants GPR56, 1383 accessions 80 variants GPR97, 54 accessions, 9 variants CCDC135, 112 accessions 10 variants speedu, 2 accessions KATNB1, 449 accessions 13 variants bawry, 13 accessions, 3 variants TEPP, 17 accessions, 4 variants C16orf57, 540 accessions 20 variants MMP15, 222 accessions 3 variants boyry, 2 accessions yosuri, 2 accessions CCDC113, 130 accessions 8 variants GINS3, 259 accessions 13 variants chosta, 1 accession spyworbu, 1 accession kawsnar, 1 accession shosta, 1 accession korsnar, 1 accession koysnar, 1 accession lasnar, 1 accession lusnar, 4 accessions losnar, 4 accessions glusta, 1 accession leesnar, 2 accessions lersnar, 1 accession lorsnar, 1 accession klarsta, 1 accession loysnar, 1 accession plorsta, 3 accessions mysnar, 1 accession varseybo, 1 accession cherpoy, 1 accession marsnar, 1 accession bloysmer, 4 accessions sperworbu, 1 accession meysnar, 1 accession skysta, 3 accessions spoyworbu, 1 accession nasnar, 2 accessions nosnar, 1 accession skeesta, 1 accession bloypoy, 6 accessions stuworbu, 1 accession flarpoy, 3 accessions stoworbu, 1 accession starworbu, 2 accessions pasnar, 1 accession lorglo, 1 accession parsnar, 1 accession steyworbu, 2 accessions sworsta, 1 accession peysnar, 1 accession flawpoy, 2 accessions stoyworbu, 1 accession poysnar, 1 accession rasnar, 2 accessions rysnar, 1 accession rosnar, 2 accessions rarsnar, 1 accession veyseybo, 1 accession reesnar, 1 accession swawworbu, 1 accession korsty, 1 accession swerworbu, 1 accession sasnar, 1 accession sysnar, 1 accession bywoybu, 1 accession sarsnar, 1 accession veysty, 1 accession dyry, 1 accession wawsty, 1 accession bowoybu, 1 accession susuma, 3 accessions soysnar, 1 accession bawwoybu, 1 accession kosnar, 1 accession swerwoy, 1 accession jeeglo, 1 accession karsnar, 1 accession keysnar, 1 accession flersta, 1 accession lysnar, 1 accession storra, 15 accessions chypoy, 1 accession spoworbu, 1 accession lawsnar, 2 accessions swyra, 1 accession chopoy, 1 accession sparworbu, 1 accession leysnar, 1 accession blarwobu, 6 accessions mosnar, 1 accession sworwoy, 2 accessions meesnar, 1 accession skasta, 6 accessions lyglo, 2 accessions skusta, 1 accession nysnar, 3 accessions vawseybo, 1 accession blorpoy, 3 accessions smosta, 1 accession smeysta, 1 accession hekori, 2 accessions spysta, 1 accession neysnar, 1 accession norsnar, 1 accession stawworbu, 1 accession verseybo, 1 accession posnar, 1 accession pawsnar, 2 accessions porsnar, 1 accession swuworbu, 1 accession swoworbu, 1 accession bawsty, 1 accession deysty, 1 accession rusnar, 1 accession hokori, 1 accession justy, 1 accession rersnar, 1 accession glawpoy, 1 accession dary, 2 accessions reysnar, 1 accession glerpoy, 1 accession roysnar, 1 accession swoyworbu, 2 accessions neysty, 1 accession bawoybu, 1 accession teysty, 1 accession susnar, 1 accession kloypoy, 1 accession sosnar, 2 accessions sisuma, 1 accession sawsnar, 1 accession buwoybu, 1 accession chusty, 1 accession barwoybu, 2 accessions gleesty, 1 accession CIAPIN1, 382 accessions 16 variants DOK4, 425 accessions, 19 variants CCDC102A, 52 accessions 4 variants yusuri, 1 accession swora, 3 accessions KIFC3, 379 accessions 40 variants CNGB1, 62 accessions, 11 variants ZNF319, 67 accessions C16orf80, 383 accessions 8 variants CSNK2A2, 503 accessions 8 variants PRSS54, 63 accessions 7 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               17 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i, .j-u, .k-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

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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