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SCP2D1 Gene

protein-coding   GIFtS: 34
GCID: GC20P018795

SCP2 Sterol-Binding Domain Containing 1

(Previous name: chromosome 20 open reading frame 79)
(Previous symbol: C20orf79)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
SCP2 Sterol-Binding Domain Containing 11 2     HSD222
C20orf791 2 3     dJ1068E13.22
Sterol Carrier Protein 2-Like Protein1 2     SCP2 Sterol-Binding Domain-Containing Protein 12
Chromosome 20 Open Reading Frame 791     

External Ids:    HGNC: 162111   Entrez Gene: 1408562   Ensembl: ENSG000001326317   UniProtKB: Q9UJQ73   

Export aliases for SCP2D1 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SCP2D1 Gene:
SCP2D1 (SCP2 sterol-binding domain containing 1) is a protein-coding gene. Diseases associated with SCP2D1 include d-bifunctional protein deficiency, and protein s deficiency. GO annotations related to this gene include sterol binding. An important paralog of this gene is SCP2.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000020.11  NC_018931.2  NT_011387.9  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SCP2D1
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SCP2D1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 20p11.23   Ensembl cytogenetic band:  20p11.23   HGNC cytogenetic band: 20p11.23

SCP2D1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SCP2D1 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P018795:  view genomic region     (about GC identifiers)

Start:
18,794,370 bp from pter      End:
18,795,036 bp from pter
Size:
667 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: SCP2D_HUMAN, Q9UJQ7 (See protein sequence)
Recommended Name: SCP2 sterol-binding domain-containing protein 1  
Size: 156 amino acids; 17663 Da
Secondary accessions: Q548A4

Explore the universe of human proteins at neXtProt for SCP2D1: NX_Q9UJQ7

Explore proteomics data for SCP2D1 at MOPED


See SCP2D1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_848578.1  
ENSEMBL proteins: 
 ENSP00000366645  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro protein domain:
 IPR003033 SCP2_sterol-bd_dom

Graphical View of Domain Structure for InterPro Entry Q9UJQ7

ProtoNet protein and cluster: Q9UJQ7

1 Blocks protein domain: IPB003033 Sterol-binding

UniProtKB/Swiss-Prot: SCP2D_HUMAN, Q9UJQ7
Similarity: Contains 1 SCP2 domain


SCP2D1 for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0032934sterol binding IEA--
     
SCP2D1 for ontologies           About GeneDecksing


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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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  --

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SCP2D1
Interactions:

    Search GeneGlobe Interaction Network for SCP2D1

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for SCP2D1 (SCP2D)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for SCP2D1 gene: 
NM_178483.2  

Unigene Cluster for SCP2D1:

SCP2 sterol-binding domain containing 1
Hs.112794  [show with all ESTs]
Unigene Representative Sequence: NM_178483
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000377428(uc002wrk.3)
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Additional mRNA sequence: 

AF418570.1 AK130970.1 AY248902.1 BC105121.1 BC112024.1 

1 DOTS entry:

DT.101975001 

Selected AceView cDNA sequences (see all 27):

AI283593 AA431698 AI200873 AI623164 AI969287 AA974140 NM_178483 AF418570 
AA833611 AY248902 AA813548 AA910166 AA609959 AK130970 AI968799 AA908942 
AA902281 AA609978 AI025344 AW003303 BX097724 AA431491 AI806942 AI269486 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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SCP2D1 expression in normal human tissues (normalized intensities)      SCP2D1 embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SCP2D1 Expression
About this image


SCP2D1 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 
 Testis (Reproductive System)
         Mature Sertoli Cells Seminiferous Tubules
SCP2D1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SCP2D1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.112794
    Custom PCR Arrays for SCP2D1
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In Situ
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals and fungi.

Orthologs for SCP2D1 gene from Selected species (see all 12)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Scp2d11 , 5 RIKEN cDNA 1700010M22 gene5
SCP2 sterol-binding domain containing 11
78.63(n)1
72.44(a)1
  2 (71.02 cM)5
663281  NM_025490.21  NP_079766.31 
 1448236565 
zebrafish
(Danio rerio)
Actinopterygii hsd17b46
hydroxysteroid (17-beta) dehydrogenase 4
9(a)
1 → many
8(397589-421306) ENSDARG00000031873
fruit fly
(Drosophila melanogaster)
Insecta Mfe26
peroxisomal Multifunctional enzyme type 2
2(a)
1 → many
X(16165007-16167858)
worm
(Caenorhabditis elegans)
Secernentea maoc-16
Protein MAOC-1 (maoc-1) mRNA, complete cds
3(a)
1 → many
II(7196276-7197495) WBGene00017123
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes FOX26
Multifunctional enzyme of the peroxisomal fatty ac...
3(a)
1 → many
XI(454352-457054) YKR009C


ENSEMBL Gene Tree for SCP2D1 (if available)
TreeFam Gene Tree for SCP2D1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for SCP2D1 gene
SCP22  HSD17B42  
1 SIMAP similar gene for SCP2D1 using alignment to 1 protein entry:     SCP2D_HUMAN:
HSD17B4

SCP2D1 for paralogs           About GeneDecksing



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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1 SNPs for SCP2D1    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 20 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs10538391,2,4
----see VAR_0243322 mis40--------

HapMap Linkage Disequilibrium report for SCP2D1 (18794370 - 18795036 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for SCP2D1: --
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing SCP2D1
DNA2.0 Custom Variant and Variant Library Synthesis for SCP2D1

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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2 diseases for SCP2D1:    About MalaCards
d-bifunctional protein deficiency    protein s deficiency


SCP2D1 for disorders           About GeneDecksing


Export disorders for SCP2D1 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for SCP2D1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SCP2D1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Fusion and fission, the evolution of sterol carrier protein-2. (PubMed id 16501878)1, 3 Edqvist J. and Blomqvist K. (J. Mol. Evol. 2006)
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  3. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (Nature 2001)
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  5. (PubMed id )2 
  6. Mutational spectrum of D-bifunctional protein deficiency and structure-based genotype-phenotype analysis. (PubMed id 16385454)9 Ferdinandusse S....Glumoff T. (Am. J. Hum. Genet. 2006)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 140856 HGNC: 16211 AceView: C20orf79 Ensembl:ENSG00000132631 euGenes: HUgn140856
ECgene: SCP2D1 H-InvDB: SCP2D1

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for SCP2D1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for SCP2D1 gene:
Search GeneIP for patents involving SCP2D1

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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