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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

B9D1 Gene

protein-coding GIFtS: 45
GCID: GC17M019244

B9 Protein Domain 1

10 related diseases
at

MalaCards

(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

Aliases
B9 Protein Domain 1¹ ²		B9²
Endothelial Precursor Protein B9¹ ²		EPPB9²
MKSR1² ³		MKS9²
MKS1-Related Protein 1² ³		B9 Domain-Containing Protein 1²

External Ids:	HGNC: 24123¹	Entrez Gene: 27077²	Ensembl: ENSG00000108641⁷	OMIM: 614144⁵	UniProtKB: Q9UPM9³

Export aliases for B9D1 gene to outside databases

Previous GC identifers: GC17M019188 GC17M018626

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

Entrez Gene summary for B9D1 Gene:

This gene encodes a B9 domain-containing protein, one of several that are involved in ciliogenesis. Alterations in

expression of this gene have been found in a family with Meckel syndrome. Meckel syndrome has been associated with at

least six different genes. This gene is located within the Smith-Magenis syndrome region on chromosome 17. Three

alternatively spliced transcript variants that encode different proteins have been described for this gene. (provided

by RefSeq, Aug 2011)

GeneCards Summary for B9D1 Gene:

B9D1 (B9 protein domain 1) is a protein-coding gene. Diseases associated with B9D1 include b9d1-related meckel syndrome, and meckel syndrome. GO annotations related to this gene include hedgehog receptor activity. An important paralog of this gene is B9D2.

UniProtKB/Swiss-Prot: B9D1_HUMAN, Q9UPM9

Function: Component of the tectonic-like complex, a complex localized at the transition zone of primary cilia and

acting as a barrier that prevents diffusion of transmembrane proteins between the cilia and plasma membranes. Required

for ciliogenesis and sonic hedgehog/SHH signaling (By similarity)

(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_000017.10 NT_010718.16 NC_018928.2

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the B9D1 gene promoter:
AML1a
Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): B9D1 promoter sequence

Search SABiosciences Chromatin IP Primers for B9D1

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat B9D1

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

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

B9D1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
B9D1 gene location

GeneLoc information about chromosome 17 GeneLoc Exon Structure

GeneLoc location for GC17M019244: view genomic region (about GC identifiers)

Start:	19,240,867 bp from pter	End:	19,281,495 bp from pter
Size:	40,629 bases	Orientation:	minus strand

(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/Swiss-Prot: B9D1_HUMAN, Q9UPM9 (See protein sequence)

Recommended Name: B9 domain-containing protein 1

Size: 204 amino acids; 22775 Da

Subunit: Part of the tectonic-like complex (also named B9 complex) (By similarity)

Subcellular location: Cytoplasm, cytoskeleton, cilium basal body. Cytoplasm, cytoskeleton, cilium axoneme.

Note=Localizes at the transition zone, a region between the basal body and the ciliary axoneme (By similarity)

Secondary accessions: Q9BU22

Alternative splicing: 2 isoforms: Q9UPM9-1 Q9UPM9-2 (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for B9D1: NX_Q9UPM9

Explore proteomics data for B9D1 at MOPED

Post-translational modifications:

View modification sites using PhosphoSitePlus

View neXtProt modification sites for NX_Q9UPM9

B9D1 Protein expression data from MOPED¹, PaxDb² and MAXQB³ : About this image

REFSEQ proteins (3 alternative transcripts):

NP_001230402.1 NP_001230404.1 NP_056496.1

ENSEMBL proteins:

ENSP00000459857 ENSP00000433359 ENSP00000378977 ENSP00000261499 ENSP00000460939

ENSP00000378978 ENSP00000458525 ENSP00000268841 ENSP00000410835 ENSP00000462565

ENSP00000463165 ENSP00000463255

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Gene Ontology (GO): 5/6 cellular component terms (GO ID links to tree view) (see all 6): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005813	centrosome	IDA	19208769
GO:0005932	microtubule basal body	IDA	19208769
GO:0016020	membrane	IEA	--
GO:0035085	cilium axoneme	IEA	--
GO:0035869	ciliary transition zone	ISS	--

B9D1 for ontologies About GeneDecksing

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

1 InterPro protein domain:

IPR010796 B9_dom

Graphical View of Domain Structure for InterPro Entry Q9UPM9

ProtoNet protein and cluster: Q9UPM9

UniProtKB/Swiss-Prot: B9D1_HUMAN, Q9UPM9

Similarity: Belongs to the B9D family

Similarity: Contains 1 B9 domain

B9D1 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,
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 Oct 2013 via Entrez Gene.)
About This Section

Molecular Function:

UniProtKB/Swiss-Prot Summary: B9D1_HUMAN, Q9UPM9

Function: Component of the tectonic-like complex, a complex localized at the transition zone of primary cilia and

acting as a barrier that prevents diffusion of transmembrane proteins between the cilia and plasma membranes. Required

for ciliogenesis and sonic hedgehog/SHH signaling (By similarity)

Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005515	protein binding	--	--
GO:0008158	hedgehog receptor activity	ISS	--

B9D1 for ontologies About GeneDecksing

Phenotypes:
15/20 MGI mutant phenotypes (inferred from 3 alleles) (MGI details for B9d1) (see all 20):

adipose tissue	behavior/neurological	cardiovascular system	craniofacial	digestive/alimentary
embryogenesis	endocrine/exocrine gland	growth/size	hematopoietic system	homeostasis/metabolism
immune system	integument	limbs/digits/tail	liver/biliary system	mortality/aging

B9D1 for phenotypes About GeneDecksing

Animal Models:
Mouse knock-out B9d1^{tm1d(EUCOMM)Wtsi} for B9D1

inGenious Targeting Laboratory - Custom generated mouse model solutions for B9D1

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In Situ Assay
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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for B9D1

(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 Central^TM Interacting Genes and Proteins Networks for B9D1

STRING Interaction Network Preview (showing 5 interactants - click image to see 14)

5/16 Interacting proteins for B9D1 (Q9UPM9^{1, 3} ENSP00000261499⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 16)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
EXOSC10	Q01780¹^,³, ENSP00000366135⁴	EBI-372535,EBI-358236 I2D: score=3 STRING: ENSP00000366135
MRPS35	P82673³	I2D: score=5
PAH	P00439³	I2D: score=5
CEP290	ENSP00000308021⁴	STRING: ENSP00000308021
TMEM216	ENSP00000381950⁴	STRING: ENSP00000381950

About this table

Gene Ontology (GO): 5/9 biological process terms (GO ID links to tree view) (see all 9): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0001701	in utero embryonic development	IEA	--
GO:0007224	smoothened signaling pathway	ISS	--
GO:0032880	regulation of protein localization	IEA	--
GO:0035051	cardiocyte differentiation	IEA	--
GO:0042384	cilium assembly	ISS	--

B9D1 for ontologies About GeneDecksing

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

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for B9D1

Search CenterWatch for drugs/clinical trials and news about B9D1

(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,
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About This Section

REFSEQ mRNAs for B9D1 gene (3 alternative transcripts):

NM_001243473.1 NM_001243475.1 NM_015681.3

Unigene Cluster for B9D1:

B9 protein domain 1

Hs.462445 [show with all ESTs]

Unigene Representative Sequence: AK293815

15 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000575403(uc010cqm.1) ENST00000461069 ENST00000395615 ENST00000261499(uc002gvk.4)

ENST00000477478(uc010vyr.2 uc010vys.2) ENST00000395616 ENST00000575478

ENST00000268841(uc010cqn.2) ENST00000440841 ENST00000477683 ENST00000574508

ENST00000582857 ENST00000487415 ENST00000468679 ENST00000476298

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Additional mRNA sequence:

AB030506.1 AK293815.1 AK297782.1 AK309320.1 BC002944.2

9 DOTS entries:

DT.440966 DT.100752236 DT.86842265 DT.95266441 DT.92420107 DT.91967891 DT.97801922 DT.95266450

DT.95266451

24/84 AceView cDNA sequences (see all 84):

AA256668 CR606056 BQ422055 CN479141 BC002944 BU684397 BM129815 AW292166

CA776227 AA243643 CK819721 CD676260 BM976857 BQ012937 BE745789 AI871276

AA431779 BQ438211 CF529572 BQ071811 AW294805 BX389591 BX507706 BF025740

GeneLoc Exon Structure

5/6 Alternative Splicing Database (ASD) splice patterns (SP) for B9D1 (see all 6) About this scheme

ExUns:	1a	·	1b	·	1c	·	1d	^	2	^	3	^	4a	·	4b	^	5a	·	5b	^	6	^	7a	·	7b	^	8a	·	8b	·	8c	^	9
SP1:																			-		-				-
SP2:																			-		-				-		-
SP3:																			-
SP4:																			-		-
SP5:

ECgene alternative splicing isoforms for B9D1

(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

B9D1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: AGGAAACTGG

About this image

See B9D1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for B9D1

SOURCE GeneReport for Unigene cluster: Hs.462445

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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)
About This Section

This gene was present in the common ancestor of animals.

Orthologs for B9D1 gene from 7/17 species (see all 17) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	B9d1^{1 , 5}	B9 protein domain 1^{1, 5}	87.91(n)¹ 94.61(a)¹		11 (37.96 cM)⁵ 27078¹ NM_013717.2¹ NP_038745.1¹ 61505144⁵
chicken (Gallus gallus)	Aves	B9D1¹	B9 protein domain 1	74.21(n) 80.53(a)		416525 XM_414829.2 XP_414829.2
lizard (Anolis carolinensis)	Reptilia	B9D1⁶	Uncharacterized protein	69(a)	1 ↔ 1	GL343618.1(403900-407663)
African clawed frog (Xenopus laevis)	Amphibia	Xl.23494²	Xenopus laevis transcribed sequence with moderate similarity to protein refNP_056496.1 (H.sapiens) B9 protein [Homo sapiens] less	77.74(n)		BJ032226.1
zebrafish (Danio rerio)	Actinopterygii	b9d1¹	B9 protein domain 1	73.91(n) 83.7(a)		554150 NM_001024373.1 NP_001019544.1
fruit fly (Drosophila melanogaster)	Insecta	CG14870¹	CG14870	49.27(n) 35.71(a)		41888 NM_142213.2 NP_650470.1
worm (Caenorhabditis elegans)	Secernentea	mksr-1¹	Protein MKSR-1	43.64(n) 29.7(a)		186954 NM_075802.1 NP_508203.1

ENSEMBL Gene Tree for B9D1 (if available)
TreeFam Gene Tree for B9D1 (if available)

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

Paralogs for B9D1 gene

B9D2²

B9D1 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) 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

SNP ID	Valid	Clinical significance	Chr 17 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs115667701^1,2	C,F	--	19228960(+)	`GGTGGC/TTTGCT`	1	--	ds500¹		1		WA	118
rs74725000^1,2	C,F	--	19229113(+)	`GAGGCG/AGCTGG`	1	--	ds500¹		1		NA	120
rs80078275^1,2	C	--	19229120(+)	`CTGGGA/GGACCC`	1	--	ds500¹		0	--	--	--	--
rs143752817^1,2		--	19229295(+)	`TGCCCA/GTTCAG`	1	--	ut3¹		0	--	--	--	--
rs190187092^1,2		--	19229344(+)	`TCTTGC/GTTACG`	1	--	ut3¹		0	--	--	--	--
rs11652712^1,2	C,F,H	--	19229388(+)	`CCCGCA/GGAAGT`	1	--	ut3¹		24		NS EA NA WA CSA	2140
rs78797942^1,2	C,F	--	19229413(+)	`AGTGAC/ATCAGG`	1	--	ut3¹		1		EA	120
rs73980009^1,2	C,F	--	19229478(+)	`GGTGGC/GTATGA`	1	--	spa¹		2		WA	120
rs72836802^1,2	C,F	--	19229511(+)	`AGCATA/GGATTT`	1	--	int¹		2		NA EA	240
rs146850709^1,2		--	19229531(+)	`AGGCCA/TGGAAT`	1	--	int¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for B9D1 (19240867 - 19281495 bp)

Structural Variations
Database of Genomic Variants (DGV) 2 variations for B9D1: About this table

Variant ID	Type	Subtype	PubMed ID
nsv907864	CNV	Loss	21882294
nsv833393	CNV	Gain+Loss	17160897

Human Gene Mutation Database (HGMD): B9D1

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing B9D1

DNA2.0 Custom Variant and Variant Library Synthesis for B9D1

(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

B9D1 for disorders About GeneDecksing

OMIM gene information: 614144 OMIM disorders: --

UniProtKB/Swiss-Prot: B9D1_HUMAN, Q9UPM9

Meckel syndrome 9 (MKS9) [MIM:614209]: A disorder characterized by a combination of renal cysts and variably

associated features including developmental anomalies of the central nervous system (typically encephalocele), hepatic

ductal dysplasia and cysts, and polydactyly. Note=The disease is caused by mutations affecting the gene represented in

this entry

10 diseases for B9D1: About MalaCards

smith magenis syndrome nephronophthisis cystic kidney polydactyly

endotheliitis hepatitis

3 diseases from the University of Copenhagen DISEASES database for B9D1:

Nephronophthisis Cystic kidney Polydactyly

Export disorders for B9D1 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 B9D1 gene, integrated from 9 sources (see all 11):
(articles sorted by number of sources associating them with B9D1)

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B9D1 is revealed as a novel Meckel syndrome (MKS) gene by targeted exon-enriched next-generation sequencing and deletion analysis. (PubMed id 21493627)^{1, 2} Hopp K.... Harris P.C. (2011)
Functional interactions between the ciliopathy-associated Meckel syndrome 1 (MKS1) protein and two novel MKS1-related (MKSR) proteins. (PubMed id 19208769)^{1, 2} Bialas N.J.... Leroux M.R. (2009)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)^{1, 3} Strausberg R.L....Marra M.A. (2002)
Charting the landscape of tandem BRCT domain-mediated protein interactions. (PubMed id 22990118)¹ Woods N.T....Monteiro A.N. (2012)
Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)¹ Povlsen L.K....Choudhary C. (2012)
A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)¹ Wagner S.A....Choudhary C. (2011)
Global identification of modular cullin-RING ligase su bstrates. (PubMed id 21963094)¹ Emanuele M.J....Elledge S.J. (2011)
Functional redundancy of the B9 proteins and nephrocystins in Caenorhabditis elegans ciliogenesis. (PubMed id 18337471)¹ Williams C.L....Yoder B.K. (2008)
A protein interaction framework for human mRNA degradation. (PubMed id 15231747)¹ Lehner B. and Sanderson C.M. (2004)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)² Gerhard D.S....Malek J. (2004)

(in PubMed, OMIM, and NCBI Bookshelf)
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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 27077	HGNC: 24123	AceView: EPPB9	Ensembl:ENSG00000108641	euGenes: HUgn27077
ECgene: B9D1	H-InvDB: B9D1

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for B9D1	Pharmacogenomics, SNPs, Pathways

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