Homo sapiens gene CH25H, encoding cholesterol 25-hydroxylase.
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SUMMARY back to top
RefSeq summary
[CH25H] This is an intronless gene that is involved in cholesterol and lipid metabolism. The encoded protein is a membrane protein and contains clusters of histidine residues essential for catalytic activity. Unlike most other sterol hydroxylases, this enzyme is a member of a small family of enzymes that utilize diiron cofactors to catalyze the hydroxylation of hydrophobic substrates. [provided by RefSeq].

RefSeq annotates one representative transcript.

AceView synopsis, each blue text links to tables and details
According to AceView, this gene is well expressed, 0.4 times the average gene in this release. The sequence of this gene is defined by 52 GenBank accessions from 49 cDNA clones, some from multiple sclerosis lesions (seen 6 times), lung (3), pancreas (3), purified pancreatic islet (3), brain (2), heart (2), kidney (2) and 10 other tissues. We annotate structural defects or features in 2 cDNA clones. There are 2 validated alternative polyadenylation sites (see the diagram).
Function: There are 9 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (Alzheimer Disease; Genetic Predisposition to Disease), proposed to participate in pathway (Primary bile acid biosynthesis) and processes (lipid metabolic process, cholesterol metabolic process, fatty acid biosynthetic process, oxidation reduction, sterol biosynthetic process). Proteins are expected to have molecular functions (steroid hydroxylase activity, cholesterol 25-hydroxylase activity, iron ion binding, metal ion binding) and to localize in various compartments (cytosol, membrane, endoplasmic reticulum, endoplasmic reticulum membrane, integral to membrane). This gene contains Fatty acid hydroxylase superfamily domain [Pfam], some transmembrane domains [Psort2].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 10, links to other databases and other names
Map: This gene CH25H maps on chromosome 10, at 10q23 according to Entrez Gene. In AceView, it covers 1.70 kb, from 90967075 to 90965380 (NCBI 37, August 2010), on the reverse strand.
Links to: , manual annotations from GAD, KEGG_00120, the SNP view, gene overviews from Entrez Gene 9023, GeneCards, expression data from 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 CH25H or C25H, LOC9023. It has been described as cholesterol 25-hydroxylase, h25OH, cholesterol 25-monooxygenase.
EC number: This gene encodes protein number: 1.14.99.38.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Ch25h (e= 10-110).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene XF985 (e=5 10-22).
The closest A.thaliana genes, according to BlastP, are the AceView genes SMO1-1 (e=6 10-15), SMO1-2 (e=5 10-14), SMO2-2 (e=6 10-14), SMO2-1 (e=3 10-13), SMO1-3 (e=9 10-13)
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
CH25H 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 0.48 0.55 0.89 0.68 8.78 0.36 3.10 4.10 0.96 0.27 0.22 30.6 3.57 1.78 1.35 1.45 0.08 0.42 3.82 1.26 0.39 0.55 0.39 0.34 0.22 0.45 0.78 1.78 0.29 0.83 0.72 1.78 1.45 3.33 0.34 0.22 0.29 3.10 3.10 0.83 0.13 1.55 0.89 0.78 0.29 10.1 7.64 0.14 0.63 2.70 0.45 1.18 0.48 1.35 0.14 0.19 3.33 0.89 1.10 1.55 0.17 0.42 2.35 0.48 0.19 1.45 0.83 0.83 2.52 1.55 0.26 1.78 0.72 0.96 2.52 0.13 0.13 0.27 0.78 0.48 0.22 0.78 1.78 0.16 0.42 1.26 0.89 0.22 1.66 0.22 1.18 1.35 0.29 1.45 0.45 3.82 1.91 0.51 0.10 0.17 0.42 3.10 0.42 1.91 0.17 0.34 0.22 0.13 1.26 0.78 0.72 3.82 6.21 0.55 2.05 6.21 1.10 28.5 0.32 1.45 0.36 0.36 0.15 0.72 0.32 2.90 0.24 0.36 2.19 8.19 0.45 1.91 0.51 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 CH25H 5' 3' encoded on minus strand of chromosome 10 from 90,967,075 to 90,965,380 100 200bp 0 1690 bp exon 1690 bp exon capped 5' end, 1 accession Validated 3' end, 2 accessions Validated 3' end, 1 accession 1690 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 Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
aAug10-unspliced 1690 bp 272 aa 26 bp 845 bp 2kb including Promoter 1690 bp 1kb

Gene neighbors and Navigator on chromosome 10q23 back to top
LIPK C P LIPN C P LIPM C R P STAMBPL1andFAS D C I R P G R R IFIT2 C I R P IFIT6PandIFIT3 D C I R P IFIT1B C R P IFIT1 D C I R P IFIT5 C I R P R R C R P ANKRD22 D C I R P ACTA2 P FASAS C R P CH25H D C R P LIPA D C R P SLC16A12 D C R P PANK1 100kb 0 LIPK, 8 accessions LIPN, 10 accessions LIPM, 28 accessions, 2 variants STAMBPL1andFAS, 407 accessions 38 variants LOC100132116, 3 accessions ploloy, 11 accessions 4 variants IFIT2, 189 accessions IFIT6PandIFIT3, 520 accessions 8 variants IFIT1B, 18 accessions 2 variants IFIT1, 525 accessions 7 variants IFIT5, 227 accessions 4 variants ployloy, 12 accessions 2 variants skoloy, 6 accessions, 2 variants bloyklarbu, 1 accession flaklarbu, 1 accession slopoby, 1 accession fluklarbu, 1 accession smupoby, 2 accessions smopoby, 2 accessions snoysho, 1 accession floneyby, 2 accessions kloyloy, 7 accessions zarfoy, 3 accessions smawpoby, 1 accession smeepoby, 1 accession smeypoby, 1 accession snapoby, 1 accession snupoby, 5 accessions snarpoby, 2 accessions sneepoby, 1 accession yotiro, 1 accession flarklarbu, 1 accession hemare, 11 accessions spapoby, 3 accessions spypoby, 1 accession flawklarbu, 1 accession spopoby, 1 accession matiro, 1 accession verdubu, 1 accession speepoby, 1 accession speypoby, 1 accession sporpoby, 3 accessions stapoby, 1 accession sparsho, 5 accessions spawsho, 3 accessions lusnu, 1 accession nurumu, 1 accession sterpoby, 1 accession speesho, 2 accessions klerdubu, 1 accession steypoby, 1 accession stoypoby, 1 accession speysho, 2 accessions gluklarbu, 1 accession glawklarbu, 1 accession snordubu, 1 accession swopoby, 2 accessions gleeklarbu, 2 accessions sporsho, 1 accession swawpoby, 1 accession beydobu, 2 accessions swoypoby, 1 accession baparby, 1 accession gloyklarbu, 1 accession skoypoby, 1 accession nudubu, 1 accession flyklarbu, 1 accession sleypoby, 1 accession slorpoby, 2 accessions sloypoby, 1 accession doysnu, 2 accessions geesnu, 1 accession snopoby, 1 accession snerpoby, 1 accession sneypoby, 2 accessions snorpoby, 1 accession gorsnu, 1 accession snoypoby, 1 accession sparpoby, 1 accession fleeklarbu, 1 accession spawpoby, 1 accession sperpoby, 3 accessions chordubu, 1 accession fleyklarbu, 1 accession spoypoby, 1 accession mitiro, 1 accession korsnu, 1 accession nirumu, 2 accessions, 2 variants koysnu, 4 accessions, 3 variants mutiro, 2 accessions, 2 variants kluglerbu, 2 accessions snotarbo, 1 accession zawfoy, 2 accessions snartarbo, 1 accession glaklarbu, 1 accession steepoby, 2 accessions lersnu, 1 accession metiro, 18 accessions spersho, 3 accessions sperneyby, 6 accessions swapoby, 1 accession swupoby, 1 accession nerumu, 1 accession speyneyby, 1 accession glerklarbu, 3 accessions sporneyby, 3 accessions spodubu, 1 accession chafoy, 3 accessions sweepoby, 2 accessions meesnu, 1 accession swerpoby, 1 accession gleyklarbu, 4 accessions norumu, 2 accessions, 2 variants skyloy, 46 accessions glorklarbu, 1 accession skarloy, 2 accessions ANKRD22, 75 accessions 2 variants ACTA2, 578 accessions 19 variants FASAS, 6 accessions CH25H, 49 accessions LIPA, 604 accessions, 33 variants SLC16A12, 37 accessions 6 variants PANK1, 132 accessions 9 variants 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 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 see the mRNA diagram, sequence and annotation, click 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 !