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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SMCR5 Gene

RNA gene   GIFtS: 30
GCID: GC17M017680

Smith-Magenis syndrome chromosome region, candidate 5 (non-protein...

(Previous names: Smith-Magenis syndrome chromosome region, candidate 5 )
 Explore 1 disease affiliated with
SMCR5 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for SMCR5    

Aliases
for SMCR5 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 3

Aliases
Smith-Magenis Syndrome Chromosome Region, Candidate 5 (Non-Protein
Coding)1 2
NCRNA000341 2
Smith-Magenis Syndrome Chromosome Region, Candidate 51

External Ids:    HGNC: 179181   Entrez Gene: 1407712   Ensembl: ENSG000002267467   UniProtKB: Q8TEV83   
ORGUL members:         
NONCODE:n406500    

Export aliases for SMCR5 gene to outside databases

Previous GC identifers: GC17M017997 GC17M019052 GC17M017623 GC17M017880 GC17M017882 GC17M017620 GC17U901068


Summaries
for SMCR5 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
  --

Genomic Views
for SMCR5 gene

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000017.10  NC_018928.1  NT_010718.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SMCR5 gene promoter:
         GATA-3   FOXF2   NRSF form 1   Brachyury   CUTL1   C/EBPalpha   c-Ets-1   HEN1   CHOP-10   HSF2   
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SMCR5


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

Ensembl cytogenetic band:  17p11.2   HGNC cytogenetic band: 17p11.2

SMCR5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMCR5 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M017680:  view genomic region     (about GC identifiers)

Start:
 17,680,000 bp from pter      End:
 17,682,843 bp from pter
Size:
 2,844 bases      Orientation:
 minus strand

Proteins
for SMCR5 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: SMCR5_HUMAN, Q8TEV8 (See protein sequence)
Recommended Name: Smith-Magenis syndrome chromosomal region candidate gene 5 protein  
Size: 140 amino acids; 15285 Da

Explore the universe of human proteins at neXtProt for SMCR5: NX_Q8TEV8

SMCR5 Protein expression data from MOPED and PaxDb: --

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Protein Domains /
Families
for SMCR5 gene

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

ProtoNet protein and cluster: Q8TEV8


Function
for SMCR5 gene

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section
miRNA
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Inhib. RNA
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In Situ Assay
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1 GenomeRNAi human phenotype for SMCR5:
 Decreased POU5F1-GFP protein e 


Pathways & Interactions
for SMCR5 gene

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SMCR5

Drugs & Compounds
for SMCR5 gene

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
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Browse Tocris compounds for SMCR5
Search CenterWatch for drugs/clinical trials and news about SMCR5 

Transcripts
for SMCR5 gene

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section
REFSEQ mRNAs for SMCR5 gene: 
NM_144774.1  

Unigene Cluster for SMCR5:

Smith-Magenis syndrome chromosome region, candidate 5 (non-protein coding)
Hs.352643  [show with all ESTs]
Unigene Representative Sequence: NR_024007
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000543475(uc010cpo.1)

miRNA
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Inhib. RNA
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Primer
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  QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SMCR5

Additional cDNA sequence: 

AF467442.1 NR_024007.1 

1 DOTS entry:

DT.97799655 

1 AceView cDNA sequence:

AF467442 

GeneLoc Exon Structure


Expression
for SMCR5 gene

(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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

Expression evidence for SMCR5:none

SMCR5 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: AAGTCAGGCT

Microarray
RNAseq (Illumina Body Map)
(100×FPKM)½
SAGE (Serial Analysis of Gene Expression)
About this image

SMCR5 expression in embryonic tissues and stem cells
Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
Stem Cell Differentiation: 1 LifeMap Cell 
NameCategory
Line H9 (WA09) (Embryonic Stem Cell)Early Embryo, Inner Cell Mass
Expression: Positive    Negative     Selective marker
Experimental details: Curated     Microarrays     In-situ hybridization

Genevestigator expression for SMCR5

SOURCE GeneReport for Unigene cluster: Hs.352643

UniProtKB/Swiss-Prot: SMCR5_HUMAN, Q8TEV8
Tissue specificity: Widely expressed

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In Situ
Assay Products: 
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Orthologs
for SMCR5 gene

(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)
About This Section
   --

ENSEMBL Gene Tree for SMCR5 (if available)
TreeFam Gene Tree for SMCR5 (if available) 

Paralogs
for SMCR5 gene

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
  --

Genomic Variants
for SMCR5 gene

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for SMCR5
     1 Inversion: 0495
SABiosciences Cancer Mutation PCR Assays
Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SMCR5
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Disorders / Diseases
for SMCR5 gene

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
SMCR5 for disorders           About GeneDecksing

1 disease for SMCR5:    About MalaCards
smith-magenis syndrome


Export disorders for SMCR5 gene to outside databases

Publications
for SMCR5 gene

(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)
About This Section

PubMed article for SMCR5 gene integrated from 9 sources:
(articles sorted by number of sources associating them with SMCR5)		    Utopia: connect your pdf to the dynamic
world of online information

  1. Genes in a refined Smith-Magenis syndrome critical deletion interval on chromosome 17p11.2 and the syntenic region of the mouse. (PubMed id 11997338)1, 2, 3 Bi W....Lupski J.R. (2002)

External Searches for SMCR5 gene

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  
  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

Genome Databases showing SMCR5 gene

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 140771 HGNC: 17918 AceView: SMCR5 Ensembl:ENSG00000226746 euGenes: HUgn140771
ECgene: SMCR5 H-InvDB: SMCR5

Other Databases showing SMCR5 gene

(According to HUGE)
About This Section
   --

Specialized Databases showing SMCR5 gene

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
PharmGKB entry for SMCR5 Pharmacogenomics, SNPs, Pathways

Intellectual Property
for SMCR5 gene

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for SMCR5 gene:
Search GeneIP for patents involving SMCR5

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



Products
for SMCR5 gene

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Advanced Cell Diagnostics
About This Section

 
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