U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Lhx6 LIM homeobox 6 [ Rattus norvegicus (Norway rat) ]

Gene ID: 311901, updated on 17-Aug-2024

Summary

Go to the top of the page Help
Official Symbol
Lhx6provided by RGD
Official Full Name
LIM homeobox 6provided by RGD
Primary source
RGD:1306174
See related
EnsemblRapid:ENSRNOG00000005996 AllianceGenome:RGD:1306174
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in forebrain neuron development and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within cell maturation and forebrain development. Predicted to be active in nucleus. Orthologous to human LHX6 (LIM homeobox 6). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Testes (RPKM 12.0), Heart (RPKM 10.7) and 9 other tissues See more
Orthologs
human mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See Lhx6 in Genome Data Viewer
Location:
3p11
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (39829846..39853681, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (19432439..19456268, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (15409349..15433504, complement)

Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene NADH:ubiquinone oxidoreductase subunit A8 Neighboring gene MORN repeat containing 5 Neighboring gene uncharacterized LOC134486080 Neighboring gene RNA binding motif protein 18 Neighboring gene mitochondrial ribosome recycling factor Neighboring gene uncharacterized LOC120101536

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. LIM homeobox 6 (Lhx6)+ neurons in the ventral zona incerta project to the core portion of the lateral supramammillary nucleus in the rat. Oh SG, et al. Brain Res, 2020 Dec 1. PMID 32931819
  2. Purification of caudal-related homeodomain transcription factor and its binding characterization. Jeong MS, et al. J Microbiol Biotechnol, 2009 Dec. PMID 20075618
  3. NKX2.1 specifies cortical interneuron fate by activating Lhx6. Du T, et al. Development, 2008 Apr. PMID 18339674
  4. Lhx6 activity is required for the normal migration and specification of cortical interneuron subtypes. Liodis P, et al. J Neurosci, 2007 Mar 21. PMID 17376969, Free PMC Article
  5. The LIM homeobox gene, L3/Lhx8, is necessary for proper development of basal forebrain cholinergic neurons. Mori T, et al. Eur J Neurosci, 2004 Jun. PMID 15217369

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Knockdown of Lhx6 during embryonic development results in neurophysiological alterations and behavioral deficits analogous to schizophrenia in adult rats.
    Title: Knockdown of Lhx6 during embryonic development results in neurophysiological alterations and behavioral deficits analogous to schizophrenia in adult rats.
  2. LIM homeobox 6 (Lhx6)+ neurons in the ventral zona incerta project to the core portion of the lateral supramammillary nucleus in the rat.
    Title: LIM homeobox 6 (Lhx6)+ neurons in the ventral zona incerta project to the core portion of the lateral supramammillary nucleus in the rat.
  3. Studied the DNA binding activity of human CDX2. Three CDX2-binding proteins were found in rat gastric tissue, and those proteins were identified to the homeobox protein Hox-D8, LIM homeobox protein 6, and SMC1L1 protein.
    Title: Purification of caudal-related homeodomain transcription factor and its binding characterization.
Submit: New GeneRIF Correction

General gene information

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables sequence-specific double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within cerebral cortex GABAergic interneuron migration ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within cerebral cortex neuron differentiation ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within cerebral cortex radially oriented cell migration ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within cerebral cortex tangential migration ISO
Inferred from Sequence Orthology
more info
  
involved_in forebrain neuron development IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within forebrain neuron development ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within forebrain neuron fate commitment ISO
Inferred from Sequence Orthology
more info
  
involved_in neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within neuron maturation ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within neuron migration ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  

General protein information

Go to the top of the page Help
Preferred Names
LIM/homeobox protein Lhx6
Names
LIM homeobox protein 6

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001107837.2 → NP_001101307.2  LIM/homeobox protein Lhx6

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000003
    UniProtKB/TrEMBL
    A6JUG7, D3ZDG6
    Related
    ENSRNOP00000008817.4, ENSRNOT00000008817.6
    Conserved Domains (3) summary
    cd09380
    Location:99 → 152
    LIM1_Lhx6; The first LIM domain of Lhx6
    cd09382
    Location:160 → 214
    LIM2_Lhx6; The second LIM domain of Lhx6
    pfam00046
    Location:252 → 305
    Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086021.1 Reference GRCr8

    Range
    39829846..39853681 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039105263.2 → XP_038961191.1  LIM/homeobox protein Lhx6 isoform X3

    Conserved Domains (3) summary
    cd09380
    Location:99 → 152
    LIM1_Lhx6; The first LIM domain of Lhx6
    cd09382
    Location:160 → 214
    LIM2_Lhx6; The second LIM domain of Lhx6
    smart00389
    Location:249 → 294
    HOX; Homeodomain

  2. XM_006234066.5 → XP_006234128.1  LIM/homeobox protein Lhx6 isoform X1

    UniProtKB/TrEMBL
    A0A8I6AN85, A6JUG6
    Related
    ENSRNOP00000097190.1, ENSRNOT00000093874.2
    Conserved Domains (3) summary
    cd09380
    Location:99 → 152
    LIM1_Lhx6; The first LIM domain of Lhx6
    cd09382
    Location:160 → 214
    LIM2_Lhx6; The second LIM domain of Lhx6
    pfam00046
    Location:252 → 304
    Homeobox; Homeobox domain

  3. XM_039105262.2 → XP_038961190.1  LIM/homeobox protein Lhx6 isoform X2

    UniProtKB/TrEMBL
    A6JUG7
    Conserved Domains (3) summary
    cd09380
    Location:70 → 123
    LIM1_Lhx6; The first LIM domain of Lhx6
    cd09382
    Location:131 → 185
    LIM2_Lhx6; The second LIM domain of Lhx6
    pfam00046
    Location:223 → 276
    Homeobox; Homeobox domain

  4. XM_063283972.1 → XP_063140042.1  LIM/homeobox protein Lhx6 isoform X5

    UniProtKB/TrEMBL
    A6JUG6

  5. XM_039105264.2 → XP_038961192.1  LIM/homeobox protein Lhx6 isoform X4

    Conserved Domains (1) summary
    cl02475
    Location:99 → 152
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools