Homo sapiens gene HSPA12B, encoding heat shock 70kD protein 12B.
SUMMARY back to top
RefSeq summary
[HSPA12B] The protein encoded by this gene contains an atypical heat shock protein 70 (Hsp70) ATPase domain and is therefore a distant member of the mammalian Hsp70 family. This gene may be involved in susceptibility to atherosclerosis. [provided by RefSeq].

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 6 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is well expressed, 1.0 times the average gene in this release. The sequence of this gene is defined by 114 GenBank accessions from 106 cDNA clones, some from breast (seen 11 times), kidney (9), placenta (9), spleen (6), heart (5), brain, cerebellum, PCR rescued clones (3), human placenta (3) and 29 other tissues. We annotate structural defects or features in 4 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 16 distinct gt-ag introns. Transcription produces 7 different mRNAs, 6 alternatively spliced variants and 1 unspliced form. There are 2 probable alternative promotors and 2 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, presence or absence of 2 cassette exons, overlapping exons with different boundaries.
Function: There are 6 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (Alzheimer Disease; oxidative stress). Proteins are expected to have molecular functions (ATP binding, nucleotide binding) and to localize in cytoplasm.
Protein coding potential: 6 spliced mRNAs putatively encode good proteins, altogether 6 different isoforms (3 complete, 1 COOH complete, 2 partial). The remaining mRNA variant (unspliced) appears not to encode a good protein. Finally proteins from this gene may be modulated by mono-methylation; 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 20, links to other databases and other names
Map: This gene HSPA12B maps on chromosome 20, at 20p13 according to Entrez Gene. In AceView, it covers 20.45 kb, from 3713314 to 3733764 (NCBI 37, August 2010), on the direct strand.
Links to: , manual annotations from GAD, PhosphoSite, the SNP view, gene overviews from Entrez Gene 116835, 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 HSPA12B, RP5-1009E24.4, C20orf60, FLJ32150, MGC131912 or dJ1009E24.2, LOC116835. It has been described as heat shock 70 kDa protein 12B, OTTHUMP00000030120.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Hspa12b (e=4 10-73).
The closest A.thaliana genes, according to BlastP, are the AceView genes CPHSC70-1 (e=7 10-04), cpHSC70-2 (e=0.018)
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 Upstream sequence Transcription
Downstream sequence
aAug10 3012 bp 689 aa 941 bp 2kb probably including promoter 20404 bp 1kb
bAug10 3157 bp 686 aa 145 bp 951 bp 2kb including Promoter 20451 bp 1kb
cAug10 3079 bp 685 aa 78 bp 943 bp 2kb including Promoter 20376 bp 1kb
dAug10 2126 bp 520 aa 433 bp 130 bp 2kb possibly including promoter 19621 bp 1kb
eAug10 1100 bp 357 aa 408 bp 2kb including Promoter 2393 bp 1kb
fAug10 572 bp 166 aa 74 bp 2kb including Promoter 12778 bp 1kb
gAug10-unspliced 525 bp 72 aa 177 bp 129 bp 2kb 525 bp 1kb

Gene neighbors and Navigator on chromosome 20p13 back to top
ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications        
Annotated mRNA diagrams back to top
Bibliography:               6 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g-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 !