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LHX6 LIM homeobox 6 [ Homo sapiens (human) ]

Gene ID: 26468, updated on 13-Mar-2020

Summary

Official Symbol
LHX6provided by HGNC
Official Full Name
LIM homeobox 6provided by HGNC
Primary source
HGNC:HGNC:21735
See related
Ensembl:ENSG00000106852 MIM:608215
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LHX6.1
Summary
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 has tandem LIM domains as well as a DNA-binding homeodomain. The protein functions as a transcription factor involved in embryogenesis and head development and is highly expressed in neural crest derived mesenchyme cells. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2017]
Expression
Broad expression in fat (RPKM 1.9), brain (RPKM 1.8) and 20 other tissues See more
Orthologs

Genomic context

See LHX6 in Genome Data Viewer
Location:
9q33.2
Exon count:
14
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (122185626..122228957, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (124964856..124991166, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene microRNA 4478 Neighboring gene NADH:ubiquinone oxidoreductase subunit A8 Neighboring gene Sharpr-MPRA regulatory region 3979 Neighboring gene MORN repeat containing 5 Neighboring gene RNA binding motif protein 18 Neighboring gene mitochondrial ribosome recycling factor Neighboring gene prostaglandin-endoperoxide synthase 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC119542, MGC119544, MGC119545

Gene Ontology Provided by GOA

Process Evidence Code Pubs
cell maturation ISS
Inferred from Sequence or Structural Similarity
more info
 
cerebral cortex GABAergic interneuron migration ISS
Inferred from Sequence or Structural Similarity
more info
 
cerebral cortex radially oriented cell migration ISS
Inferred from Sequence or Structural Similarity
more info
 
cerebral cortex tangential migration ISS
Inferred from Sequence or Structural Similarity
more info
 
forebrain neuron development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
LIM/homeobox protein Lhx6
Names
LIM homeodomain protein 6.1
LIM/homeobox protein Lhx6.1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_029683.1 RefSeqGene

    Range
    4856..31231
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001242333.2NP_001229262.1  LIM/homeobox protein Lhx6 isoform 3

    See identical proteins and their annotated locations for NP_001229262.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence and lacks a segment in the coding region, which leads to a frameshift, compared to variant 1. The resulting isoform (3) has shorter and distinct N- and C- termini compared to isoform 1.
    Source sequence(s)
    AI265821, AK126982, AK297175, AL162424, BC103936
    Consensus CDS
    CCDS56584.1
    UniProtKB/Swiss-Prot
    Q9UPM6
    Related
    ENSP00000441464.2, ENST00000541397.2
    Conserved Domains (3) summary
    cd09380
    Location:88141
    LIM1_Lhx6; The first LIM domain of Lhx6
    cd09382
    Location:149203
    LIM2_Lhx6; The second LIM domain of Lhx6
    pfam00046
    Location:241293
    Homeobox; Homeobox domain
  2. NM_001242334.2NP_001229263.1  LIM/homeobox protein Lhx6 isoform 4

    See identical proteins and their annotated locations for NP_001229263.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (4) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AI265821, AK126982, AK289827, BC103936
    Consensus CDS
    CCDS56583.1
    UniProtKB/Swiss-Prot
    Q9UPM6
    UniProtKB/TrEMBL
    A0A024R852
    Related
    ENSP00000362860.2, ENST00000373755.6
    Conserved Domains (3) summary
    cd09380
    Location:70123
    LIM1_Lhx6; The first LIM domain of Lhx6
    cd09382
    Location:131185
    LIM2_Lhx6; The second LIM domain of Lhx6
    pfam00046
    Location:223275
    Homeobox; Homeobox domain
  3. NM_001242335.1NP_001229264.1  LIM/homeobox protein Lhx6 isoform 5

    See identical proteins and their annotated locations for NP_001229264.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (5) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AI265821, AK126982
    Consensus CDS
    CCDS59144.1
    UniProtKB/Swiss-Prot
    Q9UPM6
    Related
    ENSP00000475927.1, ENST00000559895.5
    Conserved Domains (1) summary
    pfam00046
    Location:3688
    Homeobox; Homeobox domain
  4. NM_001348190.2NP_001335119.1  LIM/homeobox protein Lhx6 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (6) is shorter at the N-terminus and a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AB031042, AI265821, AK126982, AK289827
    Consensus CDS
    CCDS87683.1
    UniProtKB/Swiss-Prot
    Q9UPM6
    Related
    ENSP00000362859.2, ENST00000373754.6
    Conserved Domains (3) summary
    cd09380
    Location:70123
    LIM1_Lhx6; The first LIM domain of Lhx6
    cd09382
    Location:131185
    LIM2_Lhx6; The second LIM domain of Lhx6
    pfam00046
    Location:223275
    Homeobox; Homeobox domain
  5. NM_014368.5NP_055183.2  LIM/homeobox protein Lhx6 isoform 1

    See identical proteins and their annotated locations for NP_055183.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AI265821, AK126982, AK299709, AL162424
    Consensus CDS
    CCDS6838.2
    UniProtKB/Swiss-Prot
    Q9UPM6
    Related
    ENSP00000377854.4, ENST00000394319.8
    Conserved Domains (3) summary
    cd09380
    Location:99152
    LIM1_Lhx6; The first LIM domain of Lhx6
    cd09382
    Location:160214
    LIM2_Lhx6; The second LIM domain of Lhx6
    pfam00046
    Location:252304
    Homeobox; Homeobox domain
  6. NM_199160.4NP_954629.2  LIM/homeobox protein Lhx6 isoform 2

    See identical proteins and their annotated locations for NP_954629.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks a segment in the coding region, which leads to a frameshift, compared to variant 1. The resulting isoform (2) contains a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AI265821, AK126982, AK299709, AL162424, BC103936
    Consensus CDS
    CCDS6837.2
    UniProtKB/Swiss-Prot
    Q9UPM6
    Related
    ENSP00000340137.3, ENST00000340587.7
    Conserved Domains (3) summary
    cd09380
    Location:99152
    LIM1_Lhx6; The first LIM domain of Lhx6
    cd09382
    Location:160214
    LIM2_Lhx6; The second LIM domain of Lhx6
    pfam00046
    Location:252304
    Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    122185626..122228957 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011518521.2XP_011516823.1  LIM/homeobox protein Lhx6 isoform X1

    Conserved Domains (3) summary
    cd09380
    Location:99152
    LIM1_Lhx6; The first LIM domain of Lhx6
    cd09382
    Location:160214
    LIM2_Lhx6; The second LIM domain of Lhx6
    pfam00046
    Location:252304
    Homeobox; Homeobox domain
  2. XM_011518522.3XP_011516824.1  LIM/homeobox protein Lhx6 isoform X2

    Conserved Domains (3) summary
    cd09380
    Location:70123
    LIM1_Lhx6; The first LIM domain of Lhx6
    cd09382
    Location:131185
    LIM2_Lhx6; The second LIM domain of Lhx6
    pfam00046
    Location:223275
    Homeobox; Homeobox domain
  3. XM_005251916.3XP_005251973.1  LIM/homeobox protein Lhx6 isoform X3

    Conserved Domains (2) summary
    cd09380
    Location:99152
    LIM1_Lhx6; The first LIM domain of Lhx6
    cl02475
    Location:160214
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
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