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SMA4 Gene

pseudogene   GIFtS: 22
GCID: GC05U990086

Glucuronidase, Beta Pseudogene


  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
SMA32
b55C20.22
Glucuronidase, Beta Pseudogene2
HC95
PPSC95

External Ids:    Entrez Gene: 110392   OMIM: 1768465   

Export aliases for SMA4 gene to outside databases

Previous GC identifers: GC05P069421 GC05M069258 GC05M069550 GC05M069470 GC05M069504


(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 SMA4 Gene:
SMA4 is a pseudogene. Diseases associated with SMA4 include spinal muscular atrophy 1, and adult spinal muscular atrophy.


(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_000005.10  NT_034772.7  NC_018916.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SMA4
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SMA4


Genomic Location:
Chromosome:5   

Entrez Gene cytogenetic band: 5q13.2   

GeneLoc information about chromosome 5        


(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, Cloud-Clone Corp, and/or others.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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(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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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular3
lysosome3
cytosol1
nucleus1

(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 SMA4
Interactions:

    Search GeneGlobe Interaction Network for SMA4

(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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(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,
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 SMA4 gene (2 alternative transcripts): 
NM_006780.1  NM_021652.2  

Unigene Clusters for SMA4:

Glucuronidase, beta pseudogene
Hs.582500  [show with all ESTs], Hs.652536  [show with all ESTs], Hs.654588  [show with all ESTs]
Unigene Representative Sequences: BC067830, AK097091, BC035411
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Additional mRNA sequence: 

AK289965.1 BC035411.1 BC131740.1 DQ786286.1 NR_024054.2 U21555.1 X75940.1 X83300.1 

Selected DOTS entries (see all 39):

DT.102840494  DT.91756203  DT.95197494  DT.100759845  DT.97821308  DT.120845328  DT.91756204  DT.97810079 
DT.102839102  DT.120845151  DT.100681714  DT.75193284  DT.91756189  DT.100797356  DT.120845293  DT.120845333 
DT.91963183  DT.100797359  DT.120845051  DT.120845087  DT.95197486  DT.115455  DT.120844964  DT.120845150 

Selected AceView cDNA sequences (see all 148):

BU159152 AA779978 N50607 CA843339 AA702441 BU620019 AA557235 AA746248 
AA936501 AA367040 BM451186 AA400319 AI167341 AI003510 AA827563 AA972756 
BF111170 BQ775022 BU633204 AA287203 CA843587 AA584637 BV201241 H87257 

(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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SMA4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GAAGGCAAAT
SMA4 Expression
About this image

SMA4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SMA4 Protein Expression

SOURCE GeneReport for Unigene clusters: Hs.582500 Hs.652536 Hs.654588
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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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  --

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

(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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Selected SNPs for SMA4 (see all 201)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 5 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1916225041,2
--69426235(+) TATGAC/TTTTAG 1 -- int10--------
rs1842089191,2
--69426565(+) CAGCAG/TTTTTT 1 -- int10--------
rs1891289341,2
--69426578(+) TTTTAA/CTAGGT 1 -- int10--------
rs1810701101,2
--69442374(+) GGACTG/TCAACA 2 -- int10--------
rs1871348501,2
C--69442379(+) TCAACA/GTATGT 2 -- int10--------
rs1905030451,2
C--69442483(+) GTACAA/CTGAAT 2 -- int10--------
rs1819523731,2
C--69442503(+) TTTGAC/GATGGA 2 -- int10--------
rs1856838201,2
C--69453235(+) TATAGA/GCAGAA 2 -- int10--------
rs2014637971,2
C--69453647(+) CACCCC/TAGGTT 2 -- int10--------
rs1997149601,2
C--69453668(+) GCCTAC/TTGATC 2 -- int10--------
Structural Variations
     Database of Genomic Variants (DGV) Selected variations for SMA4 (see all 46):    About this table    
Variant IDTypeSubtypePubMed ID
nsv471489CNV Duplication19718026
dgv6094n71CNV Loss21882294
nsv881911CNV Loss21882294
nsv881768CNV Loss21882294
dgv6114n71CNV Loss21882294
nsv821643CNV Loss15273396
nsv881904CNV Loss21882294
dgv6101n71CNV Loss21882294
dgv6112n71CNV Loss21882294
dgv6102n71CNV Loss21882294

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(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.)
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OMIM gene information: 176846    OMIM disorders: --

4 diseases for SMA4:    
About MalaCards
spinal muscular atrophy 1    adult spinal muscular atrophy    juvenile spinal muscular atrophy    spinal muscular atrophy type 2


SMA4 for disorders           About GeneDecksing


Export disorders for SMA4 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 SMA4 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SMA4)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)1 Schmutz J.... Rubin E.M. (Nature 2004)
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1 Gerhard D.S.... Malek J. (Genome Res. 2004)
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
  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. Complex repetitive arrangements of gene sequence in the candidate region of the spinal muscular atropy gene in 5q13. (PubMed id 7977382)1 Theodosiou A.M.... Davies K.E. (Am. J. Hum. Genet. 1994)
  6. A rearrangement on chromosome 5 of an expressed human beta-glucuronidase pseudogene. (PubMed id 7894161)1 Sargent C.A....Affara N.A. (Mamm. Genome 1994)

(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: 11039 AceView: SMA4 euGenes: HUgn11039

(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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  --

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for SMA4 gene:
Search GeneIP for patents involving SMA4

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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