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DBX1 Gene

protein-coding   GIFtS: 37
GCID: GC11M020177

Developing Brain Homeobox 1

  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)
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Aliases
Developing Brain Homeobox 11 2
Developing Brain Homeobox Protein 12 3
Homeobox Protein DBX12

External Ids:    HGNC: 331851   Entrez Gene: 1202372   Ensembl: ENSG000001098517   UniProtKB: A6NMT03   

Export aliases for DBX1 gene to outside databases

Previous GC identifers: GC11M020135 GC11M019861


(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 DBX1 Gene:
DBX1 (developing brain homeobox 1) is a protein-coding gene. Diseases associated with DBX1 include neuronitis. GO annotations related to this gene include transcription regulatory region sequence-specific DNA binding and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is HLX.

UniProtKB/Swiss-Prot: DBX1_HUMAN, A6NMT0
Function: Could have a role in patterning the central nervous system during embryogenesis. Has a key role in
regulating the distinct phenotypic features that distinguish two major classes of ventral interneurons, V0 and V1
neurons. Regulates the transcription factor profile, neurotransmitter phenotype, intraspinal migratory path and
axonal trajectory of V0 neurons, features that differentiate them from an adjacent set of V1 neurons (By
similarity)

Gene Wiki entry for DBX1 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000011.10  NC_018922.2  NT_009237.19  
Regulatory elements:
   Regulatory transcription factor binding sites in the DBX1 gene promoter:
         E2F-4   E2F-3a   E2F-5   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   E2F-2   AREB6   E2F-1   E2F   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidDBX1 promoter sequence
   Search Chromatin IP Primers for DBX1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DBX1


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

Entrez Gene cytogenetic band: 11p15.1   Ensembl cytogenetic band:  11p15.1   HGNC cytogenetic band: 11p15.1

DBX1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DBX1 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M020177:  view genomic region     (about GC identifiers)

Start:
20,177,701 bp from pter      End:
20,182,159 bp from pter
Size:
4,459 bases      Orientation:
minus strand

(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, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: DBX1_HUMAN, A6NMT0 (See protein sequence)
Recommended Name: Homeobox protein DBX1  
Size: 343 amino acids; 37283 Da

Explore the universe of human proteins at neXtProt for DBX1: NX_A6NMT0

Explore proteomics data for DBX1 at MOPED


See DBX1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001025036.2  
ENSEMBL proteins: 
 ENSP00000436881   ENSP00000227256  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
NKL: Homeoboxes / ANTP class : NKL subclass

5 InterPro protein domains:
 IPR020479 Homeobox_metazoa
 IPR000047 HTH_motif
 IPR017970 Homeobox_CS
 IPR001356 Homeobox_dom
 IPR009057 Homeodomain-like

Graphical View of Domain Structure for InterPro Entry A6NMT0

ProtoNet protein and cluster: A6NMT0

UniProtKB/Swiss-Prot: DBX1_HUMAN, A6NMT0
Similarity: Belongs to the H2.0 homeobox family
Similarity: Contains 1 homeobox DNA-binding domain


DBX1 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, 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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Molecular Function:

     UniProtKB/Swiss-Prot Summary: DBX1_HUMAN, A6NMT0
Function: Could have a role in patterning the central nervous system during embryogenesis. Has a key role in
regulating the distinct phenotypic features that distinguish two major classes of ventral interneurons, V0 and V1
neurons. Regulates the transcription factor profile, neurotransmitter phenotype, intraspinal migratory path and
axonal trajectory of V0 neurons, features that differentiate them from an adjacent set of V1 neurons (By
similarity)

     Gene Ontology (GO): 4 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0000976transcription regulatory region sequence-specific DNA binding IEA--
GO:0003677DNA binding ----
GO:0003700sequence-specific DNA binding transcription factor activity IEA--
GO:0043565sequence-specific DNA binding ----
     
DBX1 for ontologies           About GeneDecksing


Phenotypes:
     5 MGI mutant phenotypes (inferred from 6 alleles(MGI details for Dbx1):
 homeostasis/metabolism  mortality/aging  nervous system  no phenotypic analysis  respiratory system 

DBX1 for phenotypes           About GeneDecksing

Animal Models:
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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 UniProtKB/Swiss-Prot
DBX1_HUMAN, A6NMT0: Nucleus (By similarity)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus3
cytosol2
mitochondrion2

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IEA--

DBX1 for ontologies           About GeneDecksing


(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 DBX1
Interactions:

    Search GeneGlobe Interaction Network for DBX1

Gene Ontology (GO): 4 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006355regulation of transcription, DNA-templated ----
GO:0006357regulation of transcription from RNA polymerase II promoter ----
GO:0007275multicellular organismal development IEA--
GO:0021521ventral spinal cord interneuron specification ----

DBX1 for ontologies           About GeneDecksing



(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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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for DBX1



(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,
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 DBX1 gene: 
NM_001029865.2  

Unigene Cluster for DBX1:

Developing brain homeobox 1
Hs.558604  [show with all ESTs]
Unigene Representative Sequence: NM_001029865
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000524983(uc021qey.1) ENST00000227256(uc021qez.1)
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1 DOTS entry:

DT.120695908 

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™, 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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DBX1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AAATGGCGGA
DBX1 Expression
About this image


DBX1 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 5) fully expand
 
 Neural Tube (Nervous System)    fully expand to see all 9 entries
         Ventral Spinal Cord Progenitor Cells Spinal Ventral Columns
         Metencephalon
         spinal cord/lateral wall/ventricular layer   
 
 Spinal Cord (Nervous System)
         spinal cord/lateral wall/ventricular layer   
 
 Brain (Nervous System)    fully expand to see all 2 entries
         Striatum
 
 NULL (Uncategorized)
         Neural rosettes
 
 Head Mesenchyme (Muscoskeletal System)
         Head Mesenchyme
DBX1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

DBX1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.558604
    Custom PCR Arrays for DBX1
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DBX1

(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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This gene was present in the common ancestor of chordates.

Orthologs for DBX1 gene from Selected species (see all 11)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Dbx11 , 5 developing brain homeobox 11, 5 83.78(n)1
88.66(a)1
  7 (31.44 cM)5
131721  NM_001005232.11  NP_001005232.11 
 496314995 
chicken
(Gallus gallus)
Aves DBX11 developing brain homeobox 1 76.21(n)
80.82(a)
  422976  NM_001199474.1  NP_001186403.1 
lizard
(Anolis carolinensis)
Reptilia DBX16
developing brain homeobox 1
81(a)
1 ↔ 1
1(56900615-56909724)
African clawed frog
(Xenopus laevis)
Amphibia dbx-A2 homeodomain protein dbx 75.83(n)    AF253504.1 
zebrafish
(Danio rerio)
Actinopterygii AF030285.12   -- 72.09(n)   30416  AF030285.1 


ENSEMBL Gene Tree for DBX1 (if available)
TreeFam Gene Tree for DBX1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for DBX1 gene
HLX2  DBX22  HHEX2  

DBX1 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), 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 DBX1 (see all 174)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 11 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs572949341,2
C--20104748(+) TGGTG-/GTGGTG
        
CTGGG
1 -- int11Minor allele frequency- GTGGTG:0.00NA 2
rs1123122061,2
C--20177284(+) GGGAGG/TTGAAG 1 -- ds50010--------
rs604549421,2
C,F--20177315(+) GCTGGA/CGTTAG 1 -- ds50016Minor allele frequency- C:0.19WA CSA NA 246
rs556649551,2
C,F--20177340(+) GTTCTC/TACTCC 1 -- ds50016Minor allele frequency- T:0.19WA CSA NA 246
rs1419257931,2
--20177410(+) GACCAC/GCAGAG 1 -- ds50010--------
rs1477058381,2
C,F--20177805(+) TCCTCC/TTCGGA 2 E syn12Minor allele frequency- T:0.00NA EU 5869
rs753779381,2
C--20177821(+) AGAAGA/TCCGAA 2 D V mis10--------
rs778933311,2
C--20177822(+) GAAGTA/CCGAAG 2 D Y mis10--------
rs1431117911,2
C,F--20177868(+) GGCAGC/TGGCCC 2 P syn12Minor allele frequency- T:0.00NA EU 3705
rs617328581,2
C,F--20177888(+) CGGGTC/TCCGCA 2 N D mis15Minor allele frequency- T:0.01NS NA EU 3093

HapMap Linkage Disequilibrium report for DBX1 (20177701 - 20182159 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for DBX1:    About this table    
Variant IDTypeSubtypePubMed ID
nsv467720CNV Gain19166990
nsv469939CNV Gain18288195

Site Specific Mutation Identification with PCR Assays
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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.)
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1 disease for DBX1:    
About MalaCards
neuronitis


DBX1 for disorders           About GeneDecksing

Genetic Association Database (GAD): DBX1

Export disorders for DBX1 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 DBX1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with DBX1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Control of interneuron fate in the developing spinal cord by the progenitor homeodomain protein Dbx1. (PubMed id 11239429)1, 3 Pierani A....Jessell T.M. (Neuron 2001)
  2. Developmental origin of preBAPtzinger complex respiratory neurons. (PubMed id 21048147)1 Gray P.A....Del Negro C.A. (J. Neurosci. 2010)
  3. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PubMed id 16554811)2 Taylor T.D....Sakaki Y. (Nature 2006)

(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: 120237 HGNC: 33185 Ensembl:ENSG00000109851 euGenes: HUgn120237 ECgene: DBX1
H-InvDB: DBX1

(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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NameDescription
PharmGKB entry for DBX1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for DBX1 gene:
Search GeneIP for patents involving DBX1

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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 Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

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 Search for Antibodies for DBX1 at Abcam
 See all of Abcam's Antibodies, Kits and Proteins for DBX1
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 Browse SwitchGear 3'UTR luciferase reporter plasmids for DBX1
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 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat DBX1
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for DBX1
 inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for DBX1
 LSBio Antibodies in human, mouse, rat for DBX1
Customized transgenic rodents for:
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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