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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

SBDSP1 Gene

pseudogene GIFtS: 26
GCID: GC07P072299

Shwachman-Bodian-Diamond syndrome pseudogene 1

(Previous name: Shwachman-Bodian-Diamond syndrome pseudogene )
(Previous symbol: SBDSP)

Explore 1 disease affiliated with
SBDSP1 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
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
	NCBI:BC010183
	NONCODE:n385211 n385213 n385210 n345694 n387633	see all 6
	RNAdb: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

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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000007.13 NC_018918.1 NT_007933.15 NT_079593.2

Regulatory elements:

Search SABiosciences Regulatory transcription factor binding sites for SBDSP1
Other transcription factors

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Search SABiosciences Chromatin IP Primers for SBDSP1

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 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: --

(According to 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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, 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, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 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, 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 Central^TM Interacting Genes and Proteins Networks for SBDSP1

(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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Search CenterWatch for drugs/clinical trials and news about SBDSP1

(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,
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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

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:

ENST00000453858 ENST00000456312(uc003twg.3 uc003twh.3) ENST00000437201(uc003twf.3)

ENST00000415772(uc011kel.2) ENST00000423945

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Additional cDNA sequence:

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

12 DOTS entries:

DT.100828029 DT.121057685 DT.121057811 DT.121058023 DT.100828026 DT.95306278 DT.92454584 DT.100828034

DT.100828040 DT.121057955 DT.95183804 DT.95199710

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

CA392367 CR599716 AI825990 CR607679 BQ441749 BX953301 AA768549 BM974324

AA731264 BQ016822 CR607512 CR620464 CD242956 CD242623 CR610804 AW129224

BP341762 AA662934 AW157188 AW163160 AI245572 BG201090 BG220900 BG216321

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
CGAP TAG: TTACCTAAAT

About this image
Genevestigator expression for SBDSP1

SOURCE GeneReport for Unigene cluster: Hs.585053
SABiosciences Custom PCR Arrays for SBDSP1

Primer Products:		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for SBDSP1 Browse OriGene validated miRNA SYBR primer pairs
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In Situ
Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SBDSP1

(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, 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)
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SNP ID	Valid	Clinical significance	Chr 7 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs13311663^1,2		--	68466147(+)	`TATCAC/TACTGT`	2	--	int¹		0	--	--	--	--
rs13311307^1,2		--	68466187(+)	`TAAAAC/TTGTAT`	2	--	int¹		0	--	--	--	--
rs13311724^1,2		--	68466234(+)	`GAACAC/TAAAGT`	2	--	int¹		0	--	--	--	--
rs7790745^1,2	C	--	68466447(+)	`CCTGGC/GAGCAA`	2	--	int¹		2		NA	4
rs7791253^1,2	C,F,H	--	68466805(+)	`TCGCAC/TTGGTA`	2	--	ut5¹		5		NS EA WA	538
rs7794846^1,2	C,F,H	--	68466863(+)	`GGCTGC/TAGAAC`	2	--	ut5¹		7		NS EA NA WA	538
rs7794851^1,2	C,F	--	68466881(+)	`AGCTAC/TGACGC`	2	--	ut5¹		1		WA	118
rs60740781^1,2		--	68467252(+)	`AGGGT-/AAA CCCCGAGGATG`	2	--	us2k¹		0	--	--	--	--
rs58424613^1,2		--	68467270(+)	`GACTTA/GATATC`	2	--	us2k¹		0	--	--	--	--
rs57178519^1,2		--	68467271(+)	`ACTTAA/CTATCA`	2	--	us2k¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for SBDSP1 (72299952 - 72307978 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for SBDSP1: --

SABiosciences Cancer Mutation PCR Assays

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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.)
About This Section

SBDSP1 for disorders About GeneDecksing

1 disease for SBDSP1: About MalaCards

shwachman-diamond syndrome

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

Mutations in SBDS are associated with Shwachman-Diamond syndrome. (PubMed id 12496757)^{1, 3} Boocock G.R.B.... Rommens J.M. (2003)
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)
Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. (PubMed id 15146197)¹ Brandenberger R.... Stanton L.W. (2004)
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)
Creation of genome-wide protein expression libraries using random activation of gene expression. (PubMed id 11329013)¹ Harrington J.J.... Ducar M. (2001)
Toward a complete human genome sequence. (PubMed id 9847074)¹ Wilson R. (1998)
Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)¹ Bonaldo M.F.... Soares M.B. (1996)
(PubMed id 15608161)¹⁰

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
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

Name	Description
PharmGKB entry for SBDSP1	Pharmacogenomics, SNPs, Pathways

Intellectual Property for SBDSP1 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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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, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, 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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SBDSP1 Gene

Shwachman-Bodian-Diamond syndrome pseudogene 1

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SBDSP1 Gene

Shwachman-Bodian-Diamond syndrome pseudogene 1

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