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Set Analyses:

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GBX1 Gene

protein-coding GIFtS: 44
GCID: GC07M150845

Gastrulation Brain Homeobox 1

(Previous name: gastrulation brain homeo box 1)

Search for GBX1
at

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

Quality score for the ORGUL clustered with this gene is 3

Aliases
Gastrulation Brain Homeobox 1¹ ²
Gastrulation And Brain-Specific Homeobox Protein 1² ³
Gastrulation Brain Homeo Box 1¹
Huh-17²
Homeobox Protein GBX-1²

External Ids:	HGNC: 4185¹	Entrez Gene: 2636²	Ensembl: ENSG00000164900⁷	OMIM: 603354⁵	UniProtKB: Q14549³

ORGUL members:

Export aliases for GBX1 gene to outside databases

Previous GC identifers: GC07U990039 GC07M149093 GC07M150160 GC07M150237 GC07M150283 GC07M150476 GC07M144657

(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 GBX1 Gene:

GBX1 (gastrulation brain homeobox 1) is a protein-coding gene. GO annotations related to this gene include sequence-specific DNA binding and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is DLX2.

(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_000007.14 NC_018918.2 NT_007933.16

Regulatory elements:

Regulatory transcription factor binding sites in the GBX1 gene promoter:
HNF-4alpha2 HNF-4alpha1 NF-AT NF-AT4 NF-AT2 POU2F1 POU2F1a NF-AT3 NF-AT1 ATF
Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids

Search Chromatin IP Primers for GBX1

Epigenetics:

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat GBX1

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

Entrez Gene cytogenetic band: 7q36.1 Ensembl cytogenetic band: 7q36.1 HGNC cytogenetic band: 7q36.1

GBX1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
GBX1 gene location

GeneLoc information about chromosome 7 GeneLoc Exon Structure

GeneLoc location for GC07M150845: view genomic region (about GC identifiers)

Start:	150,845,676 bp from pter	End:	150,871,832 bp from pter
Size:	26,157 bases	Orientation:	minus strand

1 alternative location:

Chr7-,CRA_TCAG 150,175,196-150,194,388

(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.,
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UniProtKB/Swiss-Prot: GBX1_HUMAN, Q14549 (See protein sequence)

Recommended Name: Homeobox protein GBX-1

Size: 363 amino acids; 37629 Da

3 PDB 3D structures from and Proteopedia for GBX1:

2M34 (3D)

2ME0 (3D)

2ME6 (3D)

Explore the universe of human proteins at neXtProt for GBX1: NX_Q14549

Explore proteomics data for GBX1 at MOPED

See GBX1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001092304.1

ENSEMBL proteins:

ENSP00000297537

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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:

HOXL: Homeoboxes / ANTP class : HOXL subclass

4 InterPro protein domains:

IPR020479 Homeobox_metazoa

IPR017970 Homeobox_CS

IPR001356 Homeobox_dom

IPR009057 Homeodomain-like

Graphical View of Domain Structure for InterPro Entry Q14549

ProtoNet protein and cluster: Q14549

1 Blocks protein domain: IPB000047 Lambda and other repressor helix-turn-helix signature

UniProtKB/Swiss-Prot: GBX1_HUMAN, Q14549

Similarity: Contains 1 homeobox DNA-binding domain

GBX1 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:

Genatlas biochemistry entry for GBX1:

mouse telencephalon expressed Gbx homolog 1,gastrulation and brain speciifc-2,homeo domain encoding gene

Gene Ontology (GO): 3 molecular function terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003677	DNA binding	--	--
GO:0003700	sequence-specific DNA binding transcription factor activity	IEA	--
GO:0043565	sequence-specific DNA binding	IEA	--

GBX1 for ontologies About GeneDecksing

Phenotypes:
2 GenomeRNAi human phenotypes for GBX1:

G0/1 arrest

Increased G1 DNA content

4 MGI mutant phenotypes (inferred from 3 alleles) (MGI details for Gbx1):

behavior/neurological

integument

nervous system

normal

GBX1 for phenotypes About GeneDecksing

Animal Models:
MGI mouse knock-out Gbx1^tm1.1Stwt for GBX1

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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

GBX1_HUMAN, Q14549: Nucleus (By similarity)

Subcellular locations from COMPARTMENTS:

Compartment	Confidence
nucleus	5

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Gene Ontology (GO): 2 cellular component terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000228	nuclear chromosome	--	--
GO:0005634	nucleus	IEA	--

GBX1 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 GBX1
Interactions:

Search GeneGlobe Interaction Network for GBX1

Gene Ontology (GO): Selected biological process terms (see all 6): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006351	transcription, DNA-templated	IEA	--
GO:0006355	regulation of transcription, DNA-templated	--	--
GO:0007628	adult walking behavior	IEA	--
GO:0019230	proprioception	IEA	--
GO:0021522	spinal cord motor neuron differentiation	IEA	--

GBX1 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

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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,
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 GBX1 gene:

NM_001098834.2

Unigene Cluster for GBX1:

Gastrulation brain homeobox 1

Hs.647114 [show with all ESTs]

Unigene Representative Sequence: NM_001098834

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

ENST00000297537(uc011kvg.2) ENST00000475831

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1 DOTS entry:

DT.121044377

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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GBX1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: TCAACAGGTT

About this image

GBX1 Protein expression data from MOPED¹, PaxDb² and MaxQB³:

About this image

GBX1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.647114

Custom PCR Arrays for GBX1

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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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This gene was present in the common ancestor of animals.

Orthologs for GBX1 gene from Selected species (see all 11) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Gbx1^{1 , 5}	gastrulation brain homeobox 1^{1, 5}	89.88(n)¹ 93.15(a)¹		5 (11.93 cM)⁵ 231044¹ NM_015739.2¹ NP_056554.1¹ 24502757⁵
chicken (Gallus gallus)	Aves	GBX1¹	gastrulation brain homeobox 1	76.62(n) 79.25(a)		395377 XM_003640629.2 XP_003640677.1
lizard (Anolis carolinensis)	Reptilia	--	--	26(a)	many ↔ many	1(87939810-87954050)
zebrafish (Danio rerio)	Actinopterygii	gbx1¹	gastrulation brain homeobox 1	67.76(n) 72.46(a)		142985 NM_174861.2 NP_777286.1
fruit fly (Drosophila melanogaster)	Insecta	unpg⁶	unplugged	28(a)	1 → many	2R(5082719-5087377)
worm (Caenorhabditis elegans)	Secernentea	ceh-12⁶	Protein CEH-12 (ceh-12) mRNA, complete cds	30(a)	1 → many	I(5840289-5841888) WBGene00000436

ENSEMBL Gene Tree for GBX1 (if available)
TreeFam Gene Tree for GBX1 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
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Paralogs for GBX1 gene

DLX2² BARX1² NKX1-1² VENTX² GBX2² BARHL1² BARHL2² MNX1²

BARX2² DLX1² DLX3² LBX2² NKX1-2² BSX² DLX5² DLX6²

DLX4² LBX1² MSX2² MSX1²

8 SIMAP similar genes for GBX1 using alignment to 1 protein entry: GBX1_HUMAN:

HMX2 HOX B6 HOXA4 HOXB1 HHEX HOXC13

GBX2 HOXD11

GBX1 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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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
				--	--	--		--	--
rs147290569^1,2	C	--	150845650(+)	`CCCTCA/GCCTTC`	1	--	ds500¹		0	--	--	--	--
rs202046564^1,2		--	150845717(+)	`GCTCCA/GCACAG`	2	R W	mis¹		0	--	--	--	--
rs201566761^1,2	C	--	150845722(+)	`GCACAG/ACAAAC`	2	/A /V	mis¹		1		EU	1323
rs199515474^1,2	C	--	150845788(+)	`CAGAAC/TGGCTG`	2	H R	mis¹		1		EU	1323
rs75176255^1,2	C,F	--	150845853(+)	`ATCTTG/TACCTG`	2	V	syn¹		1		EA	120
rs201417319^1,2	C	--	150845886(+)	`TGGGCG/AATCTG`	2	/I	syn¹		1		EU	1323
rs200785319^1,2		--	150845912(+)	`GCTCAA/GGTATT`	2	L	syn¹		0	--	--	--	--
rs200333232^1,2	C	--	150845977(+)	`TGCGGC/TGCCGT`	2	H R	mis¹		0	--	--	--	--
rs201395169^1,2	C	--	150846022(+)	`TCACCA/GGTGCC`	2	P L	mis¹		0	--	--	--	--
rs6970768^1,2	C,H	--	150846058(+)	`TTCCCT/CTTAGC`	2	/K /R	mis¹ ese³		5		NS EA NA	416

HapMap Linkage Disequilibrium report for GBX1 (150845676 - 150871832 bp)

Structural Variations
Database of Genomic Variants (DGV) 4 variations for GBX1: About this table

Variant ID	Type	Subtype	PubMed ID
dgv7547n71	CNV	Loss	21882294
nsv831188	CNV	Loss	17160897
dgv7545n71	CNV	Loss	21882294
nsv889476	CNV	Loss	21882294

Site Specific Mutation Identification with PCR Assays

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DNA2.0 Custom Variant and Variant Library Synthesis for GBX1

(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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OMIM gene information: 603354 OMIM disorders: --

GBX1 for disorders About GeneDecksing

Genetic Association Database (GAD): GBX1

Export disorders for GBX1 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 GBX1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with GBX1)

Utopia: connect your pdf to the dynamic
world of online information

The DNA sequence of human chromosome 7. (PubMed id 12853948)^{1, 2} Hillier L.W.... Wilson R.K. (Nature 2003)
Expression of a novel human homeobox-containing gene that maps to chromosome 7q36.1 in hematopoietic cells. (PubMed id 8097731)^{1, 2} Matsui T.... Kurosawa Y. (FEBS Lett. 1993)
The HOX complex neighbored by the EVX gene, as well as two other homeobox-containing genes, the GBX-class and the EN-class, are located on the same chromosomes 2 and 7 in humans. (PubMed id 7903253)^{1, 3} Matsui T.... Kurosawa Y. (FEBS Lett. 1993)
cDNA cloning and expression of the human NOBOX gene in oocytes and ovarian follicles. (PubMed id 16597639)¹ Huntriss J.... Picton H.M. (Mol. Hum. Reprod. 2006)

(in PubMed, OMIM, and NCBI Bookshelf)
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		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)
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Entrez Gene: 2636	HGNC: 4185	Ensembl:ENSG00000164900	euGenes: HUgn2636	ECgene: GBX1
H-InvDB: GBX1

(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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Name	Description
PharmGKB entry for GBX1	Pharmacogenomics, SNPs, Pathways

Intellectual Property for GBX1 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 GBX1 gene:
Search GeneIP for patents involving GBX1

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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	GenScript Custom Assay Services for GBX1		GenScript Custom overexpressing Cell Line Services for GBX1
	CloneReady with Over 120,000 Genes		Gene Synthesis: Any Gene in Any Vector
	Vector-based siRNA and miRNA, Ready for Transfection		Gene Mutant Library, Variants up to 10^11
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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat GBX1

	inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for GBX1
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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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The GeneCards human gene database gene index: 1 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

Hot genes Disease genes GBX1 gene at Home site.

Version: 3.12.142 28 July 2014
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GBX1 Gene

Gastrulation Brain Homeobox 1

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Export list of displayed genes

GBX1 Gene

Gastrulation Brain Homeobox 1

Aliasesfor GBX1 gene

Summariesfor GBX1 gene

Genomic Viewsfor GBX1 gene

Proteinsfor GBX1 gene

GBX1 Human Recombinant Protein Products:

GBX1 Antibody Products:

GBX1 Assay Products:

Domains /Familiesfor GBX1 gene

Functionfor GBX1 gene

Localizationfor GBX1 gene

Pathways & Interactionsfor GBX1 gene

Drugs & Compoundsfor GBX1 gene

Transcriptsfor GBX1 gene

Expression for GBX1 gene

Orthologsfor GBX1 gene

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Genomic Variantsfor GBX1 gene

Disorders / Diseasesfor GBX1 gene

Publicationsfor GBX1 gene

External Searches for GBX1 gene

Genome Databases showing GBX1 gene

Other Databases showing GBX1 gene

Specialized Databases showing GBX1 gene

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Aliases
for GBX1 gene

Summaries
for GBX1 gene

Genomic Views
for GBX1 gene

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for GBX1 gene

Domains /
Families
for GBX1 gene

Function
for GBX1 gene

Localization
for GBX1 gene

Pathways & Interactions
for GBX1 gene

Drugs & Compounds
for GBX1 gene

Transcripts
for GBX1 gene

Expression
for GBX1 gene

Orthologs
for GBX1 gene

Paralogs
for GBX1 gene

Genomic Variants
for GBX1 gene

Disorders / Diseases
for GBX1 gene

Publications
for GBX1 gene

Intellectual Property
for GBX1 gene

Products
for GBX1 gene