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

SBDSP1 Gene

pseudogene   GIFtS: 25
GCID: GC07P072299

Shwachman-Bodian-Diamond Syndrome Pseudogene 1

(Previous name: Shwachman-Bodian-Diamond syndrome pseudogene)
(Previous symbol: SBDSP)
  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 5

Aliases
Shwachman-Bodian-Diamond Syndrome Pseudogene 11 2
SBDSP1 2
Shwachman-Bodian-Diamond Syndrome Pseudogene1

External Ids:    HGNC: 216461   Entrez Gene: 1553702   Ensembl: ENSG000002256487   
ORGUL members:    fRNAdb10:FR335762      
NCBI13:BC010183    
NONCODE14:n385211 n385213 n387633 n385212 n345694 see all 6      
RNAdb15:LIT2060    

Export aliases for SBDSP1 gene to outside databases

Previous GC identifer: GC07P068468


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

GeneCards Summary for SBDSP1 Gene: 
SBDSP1 (Shwachman-Bodian-Diamond syndrome pseudogene 1) is a pseudogene, and is affiliated with the lncRNA class. Diseases associated with SBDSP1 include shwachman-diamond syndrome.

fRNAdb sequence ontology for SBDSP1:
mature_transcript - A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.

View fRNAdb secondary structures for SBDSP1

(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000007.13  NC_018918.2  NT_007933.15  NT_079593.2  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for SBDSP1
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SBDSP1


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

Entrez Gene cytogenetic band: 7q11.23   Ensembl cytogenetic band:  7q11.23   HGNC cytogenetic band: 7q11.23

SBDSP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SBDSP1 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07P072299:  view genomic region     (about GC identifiers)

Start:
72,299,952 bp from pter      End:
72,307,978 bp from pter
Size:
8,027 bases      Orientation:
plus strand

1 alternative location:
Chr7+,CRA_TCAG 71,632,774-71,640,800     
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SBDSP1

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB: --


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

(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,
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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Animal Models:
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(Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SBDSP1

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
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Search CenterWatch for drugs/clinical trials and news about SBDSP1

(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,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section
1 fRNAdb Secondary structure:


Unigene Cluster for SBDSP1:

Shwachman-Bodian-Diamond syndrome pseudogene 1
Hs.585053  [show with all ESTs]
Unigene Representative Sequence: NR_024110
5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000423945 ENST00000415772(uc011kel.2) ENST00000456312(uc003twg.3 uc003twh.3)
ENST00000437201(uc003twf.3) ENST00000453858
miRNA
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Additional mRNA sequence: 

BC010183.2 NR_001588.2 NR_024109.1 NR_024110.1 NR_024111.1 

13 DOTS entries:

DT.100828029  DT.121057685  DT.121057811  DT.121058023  DT.100828026  DT.95306278  DT.92454584  DT.100828034 
DT.100828040  DT.121057955  DT.121116345  DT.95183804  DT.95199710 

24/122 AceView cDNA sequences (see all 122):

BQ441749 BQ016822 CD242956 AI825990 BP341762 CA392367 CR607679 AA662934 
BM974324 BX953301 AA768549 CR620464 AW129224 AA731264 CR610804 CR599716 
CR607512 CD242623 AL571102 BE783535 BG206843 AL545336 BG182473 AL560703 

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™, 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

SBDSP1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TTACCTAAAT
SBDSP1 Expression
About this image


Genevestigator expression for SBDSP1

SOURCE GeneReport for Unigene cluster: Hs.585053
    SABiosciences Custom PCR Arrays for SBDSP1
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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)
About This Section
  --

ENSEMBL Gene Tree for SBDSP1 (if available)
TreeFam Gene Tree for SBDSP1 (if available)

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

(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) 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

10/147 SNPs in SBDSP1 are shown (see all 147)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 7 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1901952061,2
--72300872(+) ATGTTC/GCCTCA 4 -- int10--------
rs613399911,2
C,F--72300921(+) GGCCAA/GCCTGG 4 -- int14Minor allele frequency- G:0.38NA WA CSA 8
rs1825871601,2
--72300956(+) AAAAAC/TACAAA 4 -- int10--------
rs1860552011,2
--72300962(+) ACAAAA/GTTAGC 4 -- int10--------
rs1892060141,2
--72300999(+) CCCAGC/TTACTC 4 -- int10--------
rs37620231,2
C--72301058(+) AGTGAG/CCCGAG 4 -- int11Minor allele frequency- C:0.00NA 2
rs1463928241,2
--72301083(+) CTCCAG/TCCTGG 4 -- int10--------
rs556934481,2
C--72301118(+) AGGGC-/GGGGGG 4 -- int12Minor allele frequency- G:0.00NA CSA 4
rs1816699341,2
--72301185(+) CGTTCA/GTGTTG 4 -- int10--------
rs3685970001,2
C--72301201(+) ATCTCA/GATTTA 4 -- int10--------

HapMap Linkage Disequilibrium report for SBDSP1 (72299952 - 72307978 bp)

Structural Variations
     Database of Genomic Variants (DGV) 10/21 variations for SBDSP1 (see all 21):    About this table     
Variant IDTypeSubtypePubMed ID
nsv436901CNV Insertion17901297
esv33871CNV Loss17666407
dgv7323n71CNV Loss21882294
nsv5790CNV Loss18451855
esv34349CNV Gain17911159
nsv428171CNV Gain18775914
nsv888361CNV Gain21882294
esv23205CNV Gain19812545
nsv888362CNV Gain21882294
dgv7322n71CNV Gain21882294

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(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.)
About This Section
2 diseases for SBDSP1:    About MalaCards
shwachman-diamond syndrome    


SBDSP1 for disorders           About GeneDecksing


Export disorders for SBDSP1 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)
About This Section

PubMed articles for SBDSP1 gene integrated from 9 sources:
(articles sorted by number of sources associating them with SBDSP1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Mutations in SBDS are associated with Shwachman-Diamond syndrome. (PubMed id 12496757)1, 3 Boocock G.R.B.... Rommens J.M. (2003)
  2. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
  3. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. (PubMed id 15146197)1 Brandenberger R.... Stanton L.W. (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. (2002)
  5. Creation of genome-wide protein expression libraries using random activation of gene expression. (PubMed id 11329013)1 Harrington J.J.... Ducar M. (2001)
  6. Toward a complete human genome sequence. (PubMed id 9847074)1 Wilson R. (1998)
  7. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (1996)
  8. (PubMed id 15608161)10 

(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)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 155370 HGNC: 21646 AceView: SBDSP Ensembl:ENSG00000225648 euGenes: HUgn155370
ECgene: SBDSP1 H-InvDB: SBDSP1

(According to HUGE)
About This Section
  --

(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 SBDSP1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for SBDSP1 gene:
Search GeneIP for patents involving SBDSP1

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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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