LHX6 Gene
protein-coding GIFtS : 49 GCID: GC09 M124964
LIM homeobox 6
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Aliasesfor LHX6 gene
(According to
1 HGNC ,
2 Entrez Gene ,
3 UniProtKB/Swiss-Prot ,
4 UniProtKB/TrEMBL , 5 OMIM , 6 GeneLoc ,
7 Ensembl ,
8 DME ,
9 miRBase ,
and/or 10 fRNAdb )About This Section Aliases LIM Homeobox 6 1 2 LHX6.11 2 3 LIM/Homeobox Protein Lhx6.12 3 LIM Homeodomain Protein 6.12 LIM/Homeobox Protein Lhx62 LIM Homeobox Protein 63
Export aliases for LHX6 gene to outside databases Previous GC identifers: GC09M116069 GC09M116611 GC09M118418 GC09M120340 GC09M122044 GC09M124004 GC09M094579
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Summariesfor LHX6 gene (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 LHX6 : This gene encodes a member of a large protein family that contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein may function as a transcriptional regulator and may be involved in the control of differentiation and development of neural and lymphoid cells. Two alternatively spliced transcript variants encoding distinct isoforms have been described for this gene. Alternatively spliced transcript variants have been identified, but their biological validity has not been determined. (provided by RefSeq, Jul 2008) UniProtKB/Swiss-Prot: LHX6_HUMAN, Q9UPM6 Function : Probable transcription factor required for the expression of a subset of genes involved in interneuronsmigration and development. Functions in the specification of cortical interneuron subtypes and in the migration of GABAergic interneuron precursors from the subpallium to the cerebral cortex (By similarity) Gene Wiki entry for LHX6
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Genomic Viewsfor LHX6 gene
(According to
GeneLoc and/or
HGNC , and/or
Entrez Gene (NCBI build 37) ,miRBase ,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_000009.11 NC_018920.1 NT_008470.19 Regulatory elements: SABiosciences Regulatory transcription factor binding sites in the LHX6 gene promoter:NF-1 NF-1/L Sox5 STAT2 STAT3 IRF-7A CUTL1 HNF-3beta STAT1alpha Other transcription factors Search SABiosciences Chromatin IP Primers for LHX6 Epigenetics: QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human mouse rat
Genomic Location: Genomic View : UCSC Golden Path with GeneCards custom track Entrez Gene cytogenetic band: 9q33.2 Ensembl cytogenetic band: 9q33.2 HGNC cytogenetic band: 9q33.2 LHX6 Gene in genomic location: bands according to Ensembl, locations according to
Entrez Gene Ensembl GeneLoc information about chromosome 9 GeneLoc Exon Structure
GeneLoc location for GC09M124964: view genomic region
(about GC identifiers )
Start: 124,964,856 bp from pter End:
124,991,905 bp from pter
Size: 27,050 bases Orientation:
minus strand
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Proteinsfor LHX6 gene
(According to
1 UniProtKB ,
HORDE ,
neXtProt ,
Ensembl ,
and/or Reactome ,
Modification sites according to 2 PhosphoSitePlus ,
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 ,
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/Swiss-Prot: LHX6_HUMAN, Q9UPM6 See
protein sequence )Recommended Name: Size : 363 amino acids; 40045 DaSubunit : Interacts with LDB1 (via the LIM zinc-binding domains) (By similarity)Subcellular location : Nucleus (Probable)Sequence caution : Sequence=AAI03937.1; Type=Erroneous initiation; Note=Translation N-terminally extended;Sequence=AAI03938.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAB66505.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions : A6PVQ1 A6PVQ2 A8K1B2 B7Z4D0 H0YN76 Q5T7S7 Q5T7S8 Q9NTK3 Q9UPM5Alternative splicing : 6 isoforms : Q9UPM6-1 Q9UPM6-2 Q9UPM6-3 Q9UPM6-4 Q9UPM6-5 Q9UPM6-6 (No experimental confirmation available)Explore the universe of human proteins at neXtProt for LHX6: NX_Q9UPM6 Post-translational modifications:
View modification sites using PhosphoSitePlus 2 View neXtProt modification sites for NX_Q9UPM6 LHX6 Protein expression data from MOPED and PaxDb : About this image REFSEQ proteins (5 alternative transcripts): NP_001229262.1 NP_001229263.1 NP_001229264.1 NP_055183.2 NP_954629.2 ENSEMBL proteins: ENSP00000362860 ENSP00000362859 ENSP00000340137 ENSP00000377854 ENSP00000453897 ENSP00000441464 ENSP00000452811 ENSP00000453798 ENSP00000453525 ENSP00000453606 ENSP00000453896 Human Recombinant Protein Products: Gene Ontology (GO): 1 cellular component term (GO ID links to tree view) : About this table
GO ID Qualified GO term Evidence PubMed IDs GO:0005634 nucleus
IDA --
About GeneDecksing LHX6 Antibody Products: Assay Products for LHX6:
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Protein
Domains /for LHX6 gene (According to InterPro , ProtoNet ,
UniProtKB , and/or BLOCKS ,
Sets of similar genes according to GeneDecks )
About This Section About GeneDecksing 4 InterPro domains/families :
Graphical View of Domain Structure for InterPro Entry Q9UPM6 ProtoNet protein and cluster: Q9UPM6
1 Blocks protein family : IPB001781 UniProtKB/Swiss-Prot: LHX6_HUMAN, Q9UPM6 Similarity : Contains 1 homeobox DNA-binding domainSimilarity : Contains 2 LIM zinc-binding domains
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Functionfor LHX6 gene
(According to 1 UniProtKB ,
Genatlas ,
LifeMap Discovery™ ,
IUBMB , and/or
2 DME ,
Human phenotypes from GenomeRNAi ,
Animal models from MGI Mar 06 2013,
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 ,
Clones from EMD Millipore ,
OriGene ,
SwitchGear Genomics ,
GenScript ,
Sino Biological ,
DNA2.0 ,
and Vector BioLabs ,
Cell Lines from GenScript ,
LifeMap BioReagents ,
In Situ Hybridization Assays from Advanced Cell Diagnostics ,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene .)
About This Section Function Summary: UniProtKB/Swiss-Prot: LHX6_HUMAN, Q9UPM6 Function : Probable transcription factor required for the expression of a subset of genes involved in interneuronsmigration and development. Functions in the specification of cortical interneuron subtypes and in the migration of GABAergic interneuron precursors from the subpallium to the cerebral cortex (By similarity)
Clone Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human mouse rat see all 7 )human mouse rat see all 2 )OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling GenScript: all cDNA clones in your preferred vector (see all 2 ): LHX6 (NM_014368 ) Browse Sino Biological Human cDNA Clones DNA2.0 Custom Codon Optimized Gene
Synthesis Service for LHX6 Vector BioLabs ready-to-use adenovirus/AAV for human , mouse , rat LHX6
In Situ AssayAdvanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LHX6
Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view) : About this table
About GeneDecksing Animal Models: Lhx6 tm2Vpa for LHX66 MGI mutant phenotypes (inferred from 4 alleles(MGI details for Lhx6) :About GeneDecksing
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Pathways & Interactionsfor LHX6 gene
(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 1 UniProtKB ,
2 MINT ,
3 I2D , and/or
4 STRING ,
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 CentralTM Interacting Genes and Proteins Networks for LHX6 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:0006351 transcription, DNA-dependent
IEA -- GO:0006355 regulation of transcription, DNA-dependent
-- -- GO:0021799 cerebral cortex radially oriented cell migration
ISS -- GO:0021800 cerebral cortex tangential migration
ISS -- GO:0021853 cerebral cortex GABAergic interneuron migration
ISS --
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Drugs & Compoundsfor LHX6 gene (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 Tocris compounds for LHX6 LHX6
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Transcriptsfor LHX6 gene (Secondary structures according to
fRNAdb ,Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank , Entrez Gene ,
DOTS (version 10), and/or
AceView ,
transcript ids from Ensembl
with links to UCSC , GeneLoc ,
alternative splicing isoforms according to ASD and/or
ECgene ,EMD Millipore ,
OriGene ,
QIAGEN ,
shRNA from
OriGene ,
microRNA from QIAGEN ,
OriGene ,
SwitchGear Genomics ,
GenScript ,
DNA2.0 ,
Vector BioLabs ,
Primers from
OriGene ,
SABiosciences , and/or
QIAGEN
)About This Section REFSEQ mRNAs for LHX6 gene (5 alternative transcripts): NM_001242333.1 NM_001242334.1 NM_001242335.1 NM_014368.4 NM_199160.3 Unigene Cluster for LHX6:
LIM homeobox 6 Hs.103137 [show with all ESTs ] Unigene Representative Sequence: NM_001242335 12 Ensembl transcripts including schematic representations, and UCSC links where relevant : ENST00000373755 (uc010mvw.3 ) ENST00000373754 (uc022bmx.1 ) ENST00000340587 (uc004bly.4 )ENST00000394319 (uc004blx.4 ) ENST00000559895 (uc022bmw.1 ) ENST00000541397 ENST00000464484 ENST00000482062 ENST00000558672 ENST00000560152 ENST00000560485 ENST00000559529 Clone OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human mouse rat see all 7 )human mouse rat see all 2 )OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling GenScript: all cDNA clones in your preferred vector (see all 2 ): LHX6 (NM_014368 ) DNA2.0 Custom Codon Optimized Gene
Synthesis Service for LHX6 Vector BioLabs ready-to-use adenovirus/AAV for human , mouse , rat LHX6
Additional cDNA sequence: AB031041.1 AB031042.1 AK126982.1 AK289827.1 AK297175.1 AK299709.1 AK313808.1 AL136570.1 BC103936.1 BC103937.1 BC103938.1
10 DOTS entries : DT.412600 DT.97811234
DT.99992081 DT.121209120 DT.121209122 DT.40262865 DT.95364250 DT.121209119 DT.121209123 DT.121209172 24/50 AceView cDNA sequences (see all 50 ):
AL136570 AK126982 AA128312 BQ003604 NM_014368 BU540587 BX089771 AI265821 AA136365 NM_199160 AI186377 W61009 AB031042 AA913040 BM928350 BG775906 BE280401 AW629363 BV200799 BM047198 AI269647 AA136280 BQ575483 AW662166 GeneLoc Exon Structure 5/9 Alternative Splicing Database (ASD) splice patterns (SP) for LHX6 (see all 9 ) About this scheme ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b · 10c ^ 11 ^ 12a · 12b · 12c ^ 13 ^ 14a · 14b · 14c · 14d SP1 : - - - - - - - SP2 : - - - - - - - - SP3 : - - - - SP4 : SP5 :
ECgene alternative splicing isoforms for LHX6
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Expression for LHX6 gene
(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 ,SABiosciences ,
Primers from
OriGene ,
SABiosciences , and/or
QIAGEN ,
In Situ Hybridization Assays from Advanced Cell Diagnostics )
About This Section LHX6 expression in normal human tissues (normalized intensities) See probesets specificity/sensitivity at GeneAnnot About this image BioGPS CGAP TAG: TCGTGCTTTG
About this image LHX6 expression in embryonic tissues and stem cells About this table See LHX6 Protein Expression from SPIRE MOPED and PaxDB Genevestigator expression for LHX6 SOURCE GeneReport for Unigene cluster: Hs.103137 SABiosciences Custom PCR Arrays for LHX6 Primer OriGene genome-wide validated SYBR primer pairs in human mouse rat Browse OriGene validated miRNA SYBR primer pairs SABiosciences RT2 qPCR Primer Assay in human mouse rat QIAGEN QuantiTect SYBR Green Assays in human mouse rat QIAGEN QuantiFast Probe-based Assays in human mouse rat In Situ Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LHX6
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Orthologsfor LHX6 gene
(Orthologs according to
1,2 HomoloGene (2 older version, for species not in 1 newer version),
3 euGenes ,
4 SGD
,
5 MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase ,
and/or
6 Ensembl pan taxonomic compara ,
Gene Trees according to Ensembl and
TreeFam )
About This Section Orthologs for LHX6 gene from 4/16 species (see all 16 ) About this table
Organism
Taxonomic
Gene
Description
Human
Orthology
Details
chicken Aves LHX61
LIM homeobox 6
78.73(n) 84.97(a)
772259 XM_001235420.2 XP_001235421.2
zebrafish Actinopterygii lhx61
LIM homeobox 6
72.86(n) 79.6(a)
445565 NM_001004015.1 NP_001004015.1
fruit fly Insecta Awh3
transcription factor
48(a)
63F4 --
worm Secernentea lim-43
LIM-homeodomain
44(a)
X(3905023-3905852) --
ENSEMBL Gene Tree for LHX6 (if available)TreeFam Gene Tree for LHX6 (if available)
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Paralogsfor LHX6 gene (Paralogs according to
1 HomoloGene ,2 Ensembl , and 3 SIMAP , Pseudogenes according to 4 Pseudogene.org Build 68)About This Section Paralogs for LHX6 gene LMO2 2 ISL1 2 LHX2 2 LHX9 2 LMX1B 2 LMO1 2 LHX5 2 LMO4 2 LHX1 2 LMX1A 2 LMO3 2 LHX4 2 LHX3 2 LHX8 2 ISL2 2 18/26 SIMAP similar genes for LHX6 using alignment to 7 protein entries: LHX6_HUMAN (see all proteins )
(see all similar genes ):LHX8 LHX4 Lhx8 LIMD1 LHX3 LMO1 LHx4 LMO3 ISL1 LMO4 LHX1 POU6F1 TRIP6 ISL2 CSRP1 LHX2 LIMK1 WTIP About GeneDecksing
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Genomic Variantsfor LHX6 gene (SNPs/Variants according to the
1 NCBI SNP Database ,
2 Ensembl ,
3 PupaSUITE ,
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 )
About This Section Genomic Data Transcription Related Data Allele Frequencies SNP ID Valid Clinical Chr 9 pos Sequence # AA Type More # Allele Pop Total More
Browse Tocris compounds for 
Expression by the Database of Embryonic development, Stem cell research, and
Regenerative medicine 
Anatomical Compartment 
Negative
