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LHX9 LIM homeobox 9 [ Homo sapiens (human) ]

Gene ID: 56956, updated on 25-Jan-2024

Summary

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
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Genomic context

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

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

Gene Ontology Provided by GOA

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

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_001014434.2NP_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:120178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52115
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:262315
    Homeobox; Homeobox domain
  2. NM_001370213.1NP_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:129187
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:61124
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:267312
    HOX; Homeodomain
  3. NM_001410927.1NP_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_020204.3NP_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:129187
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:61124
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:271324
    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_011509781.3XP_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_054337758.1XP_054193733.1  LIM/homeobox protein Lhx9 isoform X1