Homo sapiens gene SCN2B, encoding sodium channel, voltage-gated, type II, beta.
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SUMMARY back to top
RefSeq annotates one representative transcript (NM included in AceView variant.a), 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 2 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is well expressed, 0.7 times the average gene in this release. The sequence of this gene is defined by 92 GenBank accessions from 77 cDNA clones, some from brain (seen 30 times), cerebellum (5), fetal brain (5), whole brain (5), hippocampus (4), amygdala (3), eye (3) and 25 other tissues. We annotate structural defects or features in 7 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 4 distinct introns (3 gt-ag, 1 gc-ag). Transcription produces 3 different mRNAs, 2 alternatively spliced variants and 1 unspliced form. The mRNAs appear to differ by overlapping exons with different boundaries.
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 aAug10).
Function: There are 9 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to a disease (Charcot-Marie-Tooth Disease) and proposed to participate in processes (sodium ion transport, synaptic transmission). Proteins are expected to have molecular functions (voltage-gated ion channel activity, voltage-gated sodium channel activity) and to localize in various compartments (voltage-gated sodium channel complex, extracellular space, membrane, integral to membrane). A putative protein interactor has been described (SCN1B).
Protein coding potential: 2 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (2 complete), containing Immunoglobulin V-set domain [Pfam], some transmembrane domains [Psort2]; 1 of the 2 complete proteins appears to be secreted. The remaining mRNA variant (unspliced) appears not to encode a good protein. Finally proteins from this gene may be modulated by phosphorylation; ubiquitination, 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 11, links to other databases and other names
Map: This gene SCN2B maps on chromosome 11, at 11q23 according to Entrez Gene. In AceView, it covers 13.87 kb, from 118047384 to 118033516 (NCBI 37, August 2010), on the reverse strand.
Links to: manual annotations from PhosphoSite, the SNP view, gene overviews from Entrez Gene 6327, 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 SCN2B or UNQ326/PRO386, LOC6327. It has been described as sodium channel subunit beta-2, sodium channel beta 2 subunit, neuronal voltage-gated sodium channel beta 2 subunit, sodium channel, voltage-gated, type II, beta polypeptide.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Scn2b (e=2 10-39).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene 5Q510 (e=0.51).
The closest A.thaliana gene, according to BlastP, is the AceView gene AT4G15040 (e=0.20)
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!.
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          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.
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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 4969 bp 215 aa 238 bp 4083 bp 18 bp 2kb including Promoter 13866 bp 1kb
bAug10 1175 bp 169 aa 172 bp 493 bp 2kb including Promoter 11483 bp 1kb
cAug10-unspliced 523 bp 67 aa 30 bp 289 bp 2kb including Promoter 523 bp 1kb

Gene neighbors and Navigator on chromosome 11q23 back to top
ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               9 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c-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'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !