Human Gene HSD11B1L (uc002mcp.4)
  Description: Homo sapiens hydroxysteroid (11-beta) dehydrogenase 1-like (HSD11B1L), transcript variant d, mRNA.
RefSeq Summary (NM_198708): This gene is a member of the hydroxysteroid dehydrogenase family. The encoded protein is similar to an enzyme that catalyzes the interconversion of inactive to active glucocorticoids (e.g. cortisone). Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jun 2012].
Transcript (Including UTRs)
   Position: hg19 chr19:5,680,776-5,688,534 Size: 7,759 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr19:5,686,997-5,687,956 Size: 960 Coding Exon Count: 4 

Page IndexSequence and LinksPrimersGene AllelesRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:5,680,776-5,688,534)mRNA (may differ from genome)Protein (152 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
HGNCLynxMGIPubMedUniProtKBBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 38.91 RPKM in Brain - Anterior cingulate cortex (BA24)
Total median expression: 405.01 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -417.83811-0.515 Picture PostScript Text
3' UTR -217.41578-0.376 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF00106 - short chain dehydrogenase

SCOP Domains:
51735 - NAD(P)-binding Rossmann-fold domains

ModBase Predicted Comparative 3D Structure on Q7Z5J1-7
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  BC094798 - Homo sapiens hydroxysteroid (11-beta) dehydrogenase 1-like, mRNA (cDNA clone IMAGE:4801167).
AY268351 - Homo sapiens short-chain dehydrogenase/reductase 10a (SCDR10) mRNA, complete cds; alternatively spliced.
AY313895 - Homo sapiens short-chain dehydrogenase/reductase 10f (SCDR10) mRNA, complete cds; alternatively spliced.
AY313896 - Homo sapiens short-chain dehydrogenase/reductase 10g (SCDR10) mRNA, complete cds; alternatively spliced.
AK308206 - Homo sapiens cDNA, FLJ98154.
AY313894 - Homo sapiens short-chain dehydrogenase/reductase 10e (SCDR10) mRNA, complete cds; alternatively spliced.
AY268353 - Homo sapiens short-chain dehydrogenase/reductase 10c (SCDR10) mRNA, complete cds; alternatively spliced.
BC062777 - Homo sapiens cDNA clone IMAGE:4618237, partial cds.
AY268352 - Homo sapiens short-chain dehydrogenase/reductase 10b (SCDR10) mRNA, complete cds; alternatively spliced.
AY268354 - Homo sapiens short-chain dehydrogenase/reductase 10d (SCDR10) mRNA, complete cds; alternatively spliced.
BC053546 - Homo sapiens hydroxysteroid (11-beta) dehydrogenase 1-like, mRNA (cDNA clone IMAGE:5732320), complete cds.
BC072434 - Homo sapiens hydroxysteroid (11-beta) dehydrogenase 1-like, mRNA (cDNA clone IMAGE:5729121), complete cds.
BC018336 - Homo sapiens hydroxysteroid (11-beta) dehydrogenase 1-like, mRNA (cDNA clone IMAGE:3863398), complete cds.
BC152753 - Synthetic construct Homo sapiens clone IMAGE:100015977, MGC:184149 hydroxysteroid (11-beta) dehydrogenase 1-like (HSD11B1L) mRNA, encodes complete protein.
AB528801 - Synthetic construct DNA, clone: pF1KE0267, Homo sapiens HSD11B1L gene for hydroxysteroid (11-beta) dehydrogenase 1-like protein, without stop codon, in Flexi system.
BC093950 - Homo sapiens hydroxysteroid (11-beta) dehydrogenase 1-like, mRNA (cDNA clone IMAGE:7939795), partial cds.
BC112187 - Homo sapiens hydroxysteroid (11-beta) dehydrogenase 1-like, mRNA (cDNA clone IMAGE:8327655), partial cds.
CU690982 - Synthetic construct Homo sapiens gateway clone IMAGE:100023204 5' read HSD11B1L mRNA.
KJ896145 - Synthetic construct Homo sapiens clone ccsbBroadEn_05539 HSD11B1L gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: HSD3, NM_198708, NP_941997, Q7Z5J1-7, SCDR10, uc002mcp.3
UCSC ID: uc002mcp.4
RefSeq Accession: NM_198708
Protein: Q7Z5J1-7, splice isoform of Q7Z5J1 CCDS: CCDS58642.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_198708.2
exon count: 7CDS single in 3' UTR: no RNA size: 1848
ORF size: 459CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 784.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.