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    LHX9 LIM homeobox 9 [ Homo sapiens (human) ]

    Gene ID: 56956, updated on 17-Mar-2024

    Summary

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    Official Symbol
    LHX9provided by HGNC
    Official Full Name
    LIM homeobox 9provided by HGNC
    Primary source
    HGNC:HGNC:14222
    See related
    Ensembl:ENSG00000143355 MIM:606066; AllianceGenome:HGNC:14222
    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
    Summary
    This gene encodes a member of the LIM homeobox gene family of developmentally expressed transcription factors. The encoded protein contains a homeodomain and two cysteine-rich zinc-binding LIM domains involved in protein-protein interactions. The protein is highly similar to a mouse protein that causes gonadal agenesis when inactivated, suggesting a role in gonadal development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in ovary (RPKM 2.6), testis (RPKM 0.9) and 1 other tissue See more
    Orthologs
    mouse all
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    Genomic context

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    See LHX9 in Genome Data Viewer
    Location:
    1q31.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (197912464..197935478)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (197171857..197194877)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (197881594..197904608)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene DENN domain containing 1B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1661 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1662 Neighboring gene Sharpr-MPRA regulatory region 12429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2276 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:197757007-197757507 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:197769368-197770108 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:197771590-197772329 Neighboring gene family with sequence similarity 204 member B, pseudogene Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:197779872-197780608 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:197782608-197783566 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:197783567-197784524 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:197859970-197860527 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1663 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:197887073-197887799 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:197890605-197891127 Neighboring gene chromosome 1 open reading frame 53 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:198001212-198001386 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:198025825-198026449 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2277 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2279 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2280 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2281 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2282 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2283 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2284 Neighboring gene Sharpr-MPRA regulatory region 4677 Neighboring gene proline rich 13 pseudogene 1 Neighboring gene NIMA related kinase 7 Neighboring gene VISTA enhancer hs1322 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:198283627-198284283 Neighboring gene NANOG hESC enhancer GRCh37_chr1:198392710-198393375 Neighboring gene uncharacterized LOC105371677

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Increased LHX9 expression in alveolar epithelial type 2 cells of patients with chronic obstructive pulmonary disease. Okutomo K, et al. Respir Investig, 2022 Jan. PMID 34548271
    2. Aberrant methylation and reduced expression of LHX9 in malignant gliomas of childhood. Vladimirova V, et al. Neoplasia, 2009 Jul. PMID 19568415, Free PMC Article
    3. Absence of mutations involving the LIM homeobox domain gene LHX9 in 46,XY gonadal agenesis and dysgenesis. Ottolenghi C, et al. J Clin Endocrinol Metab, 2001 Jun. PMID 11397841
    4. LHX9, a p53-binding protein, inhibits the progression of glioma by suppressing glycolysis. Luo X, et al. Aging (Albany NY), 2021 Sep 17. PMID 34536269, Free PMC Article
    5. Smad ubiquitylation regulatory factor 1 promotes LIM-homeobox gene 9 degradation and represses testosterone production in Leydig cells. Hu F, et al. FASEB J, 2018 Sep. PMID 29565736

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Transcription factor LHX9 (LIM Homeobox 9) enhances pyruvate kinase PKM2 activity to induce glycolytic metabolic reprogramming in cancer stem cells, promoting gastric cancer progression.
      Title: Transcription factor LHX9 (LIM Homeobox 9) enhances pyruvate kinase PKM2 activity to induce glycolytic metabolic reprogramming in cancer stem cells, promoting gastric cancer progression.
    2. LHX9, a p53-binding protein, inhibits the progression of glioma by suppressing glycolysis.
      Title: LHX9, a p53-binding protein, inhibits the progression of glioma by suppressing glycolysis.
    3. Increased LHX9 expression in alveolar epithelial type 2 cells of patients with chronic obstructive pulmonary disease.
      Title: Increased LHX9 expression in alveolar epithelial type 2 cells of patients with chronic obstructive pulmonary disease.
    4. that Smurf1 promotes Lhx9 ubiquitylation and is involved in testosterone production in Leydig cells directly
      Title: Smad ubiquitylation regulatory factor 1 promotes LIM-homeobox gene 9 degradation and represses testosterone production in Leydig cells.
    5. LHX9 gene is frequently silenced in pediatric malignant astrocytomas
      Title: Aberrant methylation and reduced expression of LHX9 in malignant gliomas of childhood.
    6. Lhx9 and Lhx1 serve as a binary switch in controlling the rostral versus caudal longitudinal turning of the caudal commissural axons. Lhx1 determines caudal turning and Lhx9 triggers rostral turning.
      Title: Transcriptional control of axonal guidance and sorting in dorsal interneurons by the Lim-HD proteins Lhx9 and Lhx1.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in dorsal spinal cord interneuron anterior axon guidance ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in female gonad development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in gonad morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in male gonad development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    LIM/homeobox protein Lhx9
    Names
    LIM homeobox protein 9

    NCBI Reference Sequences (RefSeq)

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    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_001014434.2 → NP_001014434.1  LIM/homeobox protein Lhx9 isoform 2

      See identical proteins and their annotated locations for NP_001014434.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1, resulting in a protein that maintains the reading frame but has a shorter N-terminus.
      Source sequence(s)
      AA316988, AJ277915, AL590115, AY273889
      Consensus CDS
      CCDS30962.1
      UniProtKB/Swiss-Prot
      Q9NQ69
      Related
      ENSP00000356360.3, ENST00000367390.7
      Conserved Domains (3) summary
      cd09377
      Location:120 → 178
      LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
      cd09469
      Location:52 → 115
      LIM1_Lhx2; The first LIM domain of Lhx2
      pfam00046
      Location:262 → 315
      Homeobox; Homeobox domain

    2. NM_001370213.1 → NP_001357142.1  LIM/homeobox protein Lhx9 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL590115
      Related
      ENSP00000356361.1, ENST00000367391.5
      Conserved Domains (3) summary
      cd09377
      Location:129 → 187
      LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
      cd09469
      Location:61 → 124
      LIM1_Lhx2; The first LIM domain of Lhx2
      smart00389
      Location:267 → 312
      HOX; Homeodomain

    3. NM_001410927.1 → NP_001397856.1  LIM/homeobox protein Lhx9 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL590115
      Consensus CDS
      CCDS91139.1
      UniProtKB/TrEMBL
      H0YL54
      Related
      ENSP00000453064.1, ENST00000561173.5

    4. NM_020204.3 → NP_064589.2  LIM/homeobox protein Lhx9 isoform 1

      See identical proteins and their annotated locations for NP_064589.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL590115, AY273889
      Consensus CDS
      CCDS1393.1
      UniProtKB/Swiss-Prot
      Q5VUE2, Q5VUE3, Q5VUE6, Q86UH2, Q9BYU6, Q9NQ69, Q9NQ70
      Related
      ENSP00000356357.4, ENST00000367387.6
      Conserved Domains (3) summary
      cd09377
      Location:129 → 187
      LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
      cd09469
      Location:61 → 124
      LIM1_Lhx2; The first LIM domain of Lhx2
      pfam00046
      Location:271 → 324
      Homeobox; Homeobox domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      197912464..197935478
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011509781.3 → XP_011508083.2  LIM/homeobox protein Lhx9 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      197171857..197194877
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337758.1 → XP_054193733.1  LIM/homeobox protein Lhx9 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NQ69.3 GenPept UniProtKB/Swiss-Prot:Q9NQ69

    Gene LinkOut

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

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