LHX9 LIM homeobox 9 [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

Location:: 1q31.3

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (197912464..197935478)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (197171857..197194877)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (197881594..197904608)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
LHX9 gene is frequently silenced in pediatric malignant astrocytomas
Title: Aberrant methylation and reduced expression of LHX9 in malignant gliomas of childhood.
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.

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Lhx9 (e-PCR), detects polymorphism
- UniSTS:525919

LHX9_2217 (e-PCR)
- UniSTS:280824

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
located_in 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)

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
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
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
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