lhx9 LIM homeobox 9 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: lhx9provided by ZNC
Official Full Name: LIM homeobox 9provided by ZNC
Primary source: ZFIN:ZDB-GENE-050417-210
See related: Ensembl:ENSDARG00000056979 AllianceGenome:ZFIN:ZDB-GENE-050417-210
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: zgc:112196; si:dkey-121a9.2
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. Acts upstream of or within neuron fate specification and thalamus development. Predicted to be active in nucleus. Is expressed in several structures, including brain; forebrain neural keel; hypocretin-secreting neurons; pericardial region; and retina. Orthologous to human LHX9 (LIM homeobox 9). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 22

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	22	NC_007133.7 (23242814..23255946, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	22	NC_007133.6 (23228034..23241119, complement)

Chromosome 22 - NC_007133.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Lhx9 is sufficient to specify Hcrt-expressing neurons in the developing mouse hypothalamus.
Title: Evolutionarily conserved regulation of hypocretin neuron specification by Lhx9.
Lack of Lhx2/Lhx9 function as well as increased Wnt signaling alter the expression of the thalamus specific cell adhesion factor pcdh10b and lead subsequently to a striking anterior-posterior disorganization of the caudal forebrain.
Title: Lhx2 and Lhx9 determine neuronal differentiation and compartition in the caudal forebrain by regulating Wnt signaling.

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General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation 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

Process	Evidence Code	Pubs
involved_in dorsal spinal cord interneuron anterior axon guidance	ISS Inferred from Sequence or Structural Similarity 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
acts_upstream_of_or_within neuron fate specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within thalamus development	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: LIM/homeobox protein Lhx9

Names: LIM homeodomain type transcription factor Lhx9

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_001017710.2 → NP_001017710.2 LIM/homeobox protein Lhx9 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) includes an alternate 3' terminal exon compared to variant 2. The encoded isoform (1) has a shorter and distinct C-terminus compared to isoform 2.

Source sequence(s)

BX004971, EH447961, EH473801

UniProtKB/TrEMBL

A0A2U3TWB7, A0A8M1N568

Related

ENSDARP00000143543.2, ENSDART00000175556.2

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 → 312

Homeobox; Homeobox domain
NM_001037243.2 → NP_001032320.2 LIM/homeobox protein Lhx9 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) represents the longer transcript and encodes the longer isoform (2).

Source sequence(s)

BC163023, BX004971, EH447961

UniProtKB/Swiss-Prot

Q1LWV4, Q3LHM3

Related

ENSDARP00000054806.5, ENSDART00000054807.6

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 → 323

Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007133.7 Reference GRCz11 Primary Assembly

Range

23242814..23255946 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017353139.3 → XP_017208628.1 LIM/homeobox protein Lhx9 isoform X1

UniProtKB/Swiss-Prot

Q1LWV4, Q3LHM3

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 → 323

Homeobox; Homeobox domain
XM_021469324.2 → XP_021324999.1 LIM/homeobox protein Lhx9 isoform X2

UniProtKB/TrEMBL

A0A8M9PJJ4

Conserved Domains (3) summary

cd09377
Location:128 → 186

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:270 → 322

Homeobox; Homeobox domain