Homo sapiens gene SC5DL, encoding sterol-C5-desaturase (ERG3 delta-5-desaturase homolog, S. cerevisiae)-like.
TABLE OF CONTENTS / OPEN CLOSE ALL PARAGRAPHS
SUMMARY back to top
RefSeq summary
[SC5DL] This gene encodes an enzyme of cholesterol biosynthesis. The encoded protein catalyzes the conversion of lathosterol into 7-dehydrocholesterol. Mutations in this gene have been associated with lathosterolosis. Alternatively spliced transcript variants encoding the same protein have been described. [provided by RefSeq].

RefSeq annotates 2 representative transcripts (NM included in AceView variants .a and .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 5 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 2.6 times the average gene in this release. The sequence of this gene is defined by 663 GenBank accessions, some from brain (seen 33 times), hippocampus (12), kidney (9), caudate nucleus (8), amygdala (7), eye (7), liver (7) and 94 other tissues. We annotate structural defects or features in 22 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 6 distinct gt-ag introns. Transcription produces 8 different mRNAs, 5 alternatively spliced variants and 3 unspliced forms. There are 3 probable alternative promotors, 2 non overlapping alternative last exons and 11 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, 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 bAug10).
Function: There are 14 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (OMIM: Lathosterolosis; Other sources: Cholesterol, HDL/blood*; Smith-Lemli-Opitz syndrome), proposed to participate in pathways (Metabolic pathways, Steroid biosynthesis) and processes (lipid metabolic process, fatty acid biosynthetic process, oxidation reduction, sterol biosynthetic process). Proteins are expected to have molecular functions (C-5 sterol desaturase activity, iron ion binding, lathosterol oxidase activity, oxidoreductase activity) and to localize in various compartments (endoplasmic reticulum membrane, integral to membrane).
Protein coding potential: 4 spliced and the unspliced mRNAs putatively encode good proteins, altogether 4 different isoforms (3 complete, 1 COOH complete), some containing Fatty acid hydroxylase superfamily 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 11, links to other databases and other names
Map: This gene SC5DL maps on chromosome 11, at 11q23.3 according to Entrez Gene. In AceView, it covers 20.96 kb, from 121163163 to 121184124 (NCBI 37, August 2010), on the direct strand.
Links to: manual annotations from OMIM_607330, GAD, KEGG_00100, KEGG_01100, the SNP view, gene overviews from Entrez Gene 6309, 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 SC5DL, ERG3, SC5D, S5DES or LOC6309, darlorby. It has been described as lathosterol oxidase, C-5 sterol desaturase, lathosterol 5-desaturase, lathosterol dehydrogenase, delta(7)-sterol 5-desaturase, fungal ERG3, delta-5-desaturase-like, 3beta-hydroxysteroid-delta5-desaturase.
EC number: This gene encodes protein number: 1.14.21.6.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Sc5d (e= 10-150).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes 2I681 (e=10-05), 2I679 (e=2 10-05), XF985 (e=2 10-04).
The closest A.thaliana genes, according to BlastP, are the AceView genes STE1 (e=10-25), AT3G02590 (e=2 10-24)
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
SC5DL 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 4.39 6.65 12.4 99.3 11.6 7.13 7.13 8.19 8.19 6.21 7.13 70.2 17.6 23.2 46.3 151 28.5 20.2 7.13 28.5 24.8 8.78 10.8 5.40 3.82 4.71 3.57 1.18 1.35 1.78 8.19 17.6 8.78 17.6 9.41 5.40 114 228 140 1.66 13.3 21.6 12.4 6.65 12.4 35.1 5.04 5.40 5.79 7.13 11.6 32.8 5.79 8.78 4.71 1.66 3.33 6.21 2.90 49.7 40.3 9.41 10.8 14.3 20.2 4.71 18.8 9.41 12.4 7.13 8.78 4.71 4.10 7.64 4.71 4.10 11.6 11.6 14.3 6.21 6.21 4.71 4.10 3.82 10.1 5.79 10.1 4.10 18.8 17.6 8.78 6.21 4.10 10.1 65.5 7.13 4.71 2.70 3.57 2.52 131 5.40 10.8 12.4 2.05 3.33 10.1 3.82 10.1 3.57 8.78 10.1 8.19 6.21 13.3 92.7 2.35 5.04 4.71 10.8 10.8 8.19 3.57 21.6 2.52 12.4 92.7 0.83 2.35 6.21 4.39 10.8 9.41 2.35 6.21 8.19 2.52 46.3 6.21 4.71 23.2 3.82 10.8 61.1 9.41 7.13 3.33 5.04 7.13 7.13 2.05 8.19 16.4 3.57 5.79 3.57 2.05 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!.
Read more...
          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 SC5DL 5' 3' encoded on plus strand of chromosome 11 from 121,163,163 to 121,184,124 1151 63438 45774 59038 a [NM] 21578 63438 45774 59038 b [NM] 21578 63438 45774 c g-u d-u 142 59038 e 21578 f h-u 1 2kb 0 227 bp exon 10287 bp [gt-ag] intron 7 GenBank accessions 1144 RNA-seq supporting reads 112 UHR pooled cells 410 Brain 20 Blood 580 Neuroblastoma 22 Other (also 94 Primates bodymap) 220 bp exon 220 bp exon 775 bp [gt-ag] intron 141 GenBank accessions 63297 RNA-seq supporting reads 12236 UHR pooled cells 17114 Brain 2885 Blood 29947 Neuroblastoma 1115 Other (also 27107 Primates bodymap) 133 bp exon 1892 bp [gt-ag] intron 141 GenBank accessions 45633 RNA-seq supporting reads 8296 UHR pooled cells 12175 Brain 1848 Blood 22033 Neuroblastoma 1281 Other (also 19771 Primates bodymap) 101 bp exon 570 bp [gt-ag] intron 123 GenBank accessions 58915 RNA-seq supporting reads 10813 UHR pooled cells 15915 Brain 2463 Blood 28359 Neuroblastoma 1365 Other (also 28873 Primates bodymap) 6354 bp exon 7 accessions, NM_001024956.2 some from amygdala (seen once) lung (once), lung, small cell carcinoma (once) small cell carcinoma (once) thymus (once) capped 5' end, 3 accessions Validated 3' end, 1 accession 6354 bp exon 363 bp exon 363 bp exon 111 bp uORF 363 bp exon 10549 bp [gt-ag] intron 130 GenBank accessions 21448 RNA-seq supporting reads 3657 UHR pooled cells 5498 Brain 994 Blood 10678 Neuroblastoma 621 Other (also 3061 Primates bodymap) 220 bp exon 220 bp exon 220 bp exon 775 bp [gt-ag] intron 141 GenBank accessions 63297 RNA-seq supporting reads 12236 UHR pooled cells 17114 Brain 2885 Blood 29947 Neuroblastoma 1115 Other (also 27107 Primates bodymap) 133 bp exon 133 bp exon 1892 bp [gt-ag] intron 141 GenBank accessions 45633 RNA-seq supporting reads 8296 UHR pooled cells 12175 Brain 1848 Blood 22033 Neuroblastoma 1281 Other (also 19771 Primates bodymap) 101 bp exon 101 bp exon 570 bp [gt-ag] intron 123 GenBank accessions 58915 RNA-seq supporting reads 10813 UHR pooled cells 15915 Brain 2463 Blood 28359 Neuroblastoma 1365 Other (also 28873 Primates bodymap) 6354 bp exon 6354 bp exon 145 accessions, NM_006918.4 some from brain (seen 21 times) hippocampus (11), caudate nucleus (8) amygdala (6), substantia nigra (6) capped 5' end, 82 accessions Validated 3' end, 3 accessions Validated 3' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 1 accession 6354 bp exon 56 bp exon 10549 bp [gt-ag] intron 130 GenBank accessions 21448 RNA-seq supporting reads 3657 UHR pooled cells 5498 Brain 994 Blood 10678 Neuroblastoma 621 Other (also 3061 Primates bodymap) 220 bp exon 220 bp exon 775 bp [gt-ag] intron 141 GenBank accessions 63297 RNA-seq supporting reads 12236 UHR pooled cells 17114 Brain 2885 Blood 29947 Neuroblastoma 1115 Other (also 27107 Primates bodymap) 133 bp exon 1892 bp [gt-ag] intron 141 GenBank accessions 45633 RNA-seq supporting reads 8296 UHR pooled cells 12175 Brain 1848 Blood 22033 Neuroblastoma 1281 Other (also 19771 Primates bodymap) 2279 bp exon 10 accessions, some from whole brain (seen 5 times) testis (2), brain (once) total brain (once) Validated 3' end, 1 accession 2279 bp exon 1753 bp exon 1753 bp exon 49 accessions, some from brain (seen 6 times) pooled human melanocyte fetal heart, andpregnant uterus (4) uterus (4), kidney (3) lung (3) capped 5' end, 1 accession Validated 3' end, 10 accessions 1753 bp exon 692 bp exon 692 bp exon 1 accession from endometrium adenocarcinoma cell line from uterus 692 bp exon 109 bp exon 1965 bp [gt-ag] intron 1 GenBank accession 141 RNA-seq supporting reads 15 UHR pooled cells 25 Brain 4 Blood 96 Neuroblastoma 1 Other (also 8 Primates bodymap) 28 bp exon 570 bp [gt-ag] intron 123 GenBank accessions 58915 RNA-seq supporting reads 10813 UHR pooled cells 15915 Brain 2463 Blood 28359 Neuroblastoma 1365 Other (also 28873 Primates bodymap) 4280 bp exon 67 accessions, some from pancreas (seen 6 times) brain (5), colon (4) skin (4), breast normal (3) Validated 3' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 1 accession 4280 bp exon 46 bp exon 10549 bp [gt-ag] intron 130 GenBank accessions 21448 RNA-seq supporting reads 3657 UHR pooled cells 5498 Brain 994 Blood 10678 Neuroblastoma 621 Other (also 3061 Primates bodymap) 2345 bp exon 2345 bp exon 3 accessions, some from placenta (seen once) capped 5' end, 2 accessions 2345 bp exon 571 bp exon 571 bp exon 1 accession from liver 571 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.
Read more...
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 7035 bp 299 aa 237 bp 5898 bp 2kb including Promoter 20559 bp 1kb
bAug10 7171 bp 299 aa 373 bp 5898 bp 108 bp 2kb including Promoter 20957 bp 1kb
cAug10 2688 bp 209 aa 66 bp 1992 bp 2kb probably including promoter 15904 bp 1kb
dAug10-unspliced 692 bp 150 aa 219 bp 20 bp 2kb possibly including promoter 692 bp 1kb
eAug10 4417 bp 92 aa 4138 bp 2kb 6952 bp 1kb
fAug10 2391 bp 87 aa 56 bp 2071 bp 2kb including Promoter 12940 bp 1kb
gAug10-unspliced 1753 bp 44 aa 552 bp 1066 bp 2kb including Promoter 1753 bp 1kb
hAug10-unspliced 571 bp 78 aa 121 bp 213 bp 2kb 571 bp 1kb

Gene neighbors and Navigator on chromosome 11q23.3 back to top
SC5DL Title gene SC5DL, encoding sterol-C5-desaturase (ERG3 delta-5-desaturase homolog, S. cerevisiae)-like. Summary [RefSeq Summary SC5DL] This gene encodes an enzyme of cholesterol biosynthesis. The encoded protein catalyzes the conversion of lathosterol into 7-dehydrocholesterol. Mutations in this gene have been associated with lathosterolosis. Alternatively spliced transcript variants encoding the same protein have been described. [provided by RefSeq] Transcribed_gene SC5DL.aAug10 SC5DL.dAug10 Product -----> 10 NewName 11_121163163 NewNameOld darlorby GeneId 6309 Other_geneId 6309 LocusLink SC5DL Unigene Hs.287749 Type Spliced_gene Molecular -----> 9 Genetic -----> 7 Expression GO_c_psort endoplasmic reticulum membrane SC5DL.bAug10 SC5DL.cAug10 SC5DL.aAug10 Go_c_iea membrane IEA integral to membrane IEA endoplasmic reticulum membrane IEA endoplasmic reticulum IEA MicroArray UKv4_A_23_P372888 UKv4_A_23_P98446 UKv4_A_32_P41026 Regulation Pastille_regulation pastille_regulation_structure pastille_regulation_Valid3p pastille_regulation_uORF Reference -----> 14 Structure -----> 7 Position Balise Map 11 IntMap 11 121163163 121184124 Cytogenetic 11q23.3 SMAP S_Parent Genomic_sequence t11_NT_033899.8_41 Quit Update Attach... Biblio ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               14 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d-u, .e, .f, .g-u, .h-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DC

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 !