Lhx9 LIM homeobox 9 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Lhx9provided by RGD
Official Full Name: LIM homeobox 9provided by RGD
Primary source: RGD:727956
See related: EnsemblRapid:ENSRNOG00000010357 AllianceGenome:RGD:727956
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
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. Predicted to be involved in dorsal spinal cord interneuron anterior axon guidance; negative regulation of DNA-templated transcription; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within cell population proliferation and gonad development. Predicted to be active in nucleus. Orthologous to human LHX9 (LIM homeobox 9). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Brain (RPKM 4.9), Testes (RPKM 2.0) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 13q13

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (52941207..52961436, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (50389052..50409947, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (55854543..55879305, complement)

Chromosome 13 - NC_086031.1 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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Lhx9 and Lhx9alpha isoforms could be implicated in regulating various aspects of neuronal differentiation
Title: Lhx9 and lhx9alpha: differential biochemical properties and effects on neuronal differentiation.

Submit: New GeneRIF Correction

General gene information

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Markers

Lhx9 (e-PCR), detects polymorphism
- UniSTS:464679

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

BE117391 (e-PCR)
- UniSTS:248671

Lhx9 (e-PCR), detects polymorphism
- UniSTS:507026

RH144410 (e-PCR)
- UniSTS:233655

Gene Ontology Provided by RGD

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
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in dorsal spinal cord interneuron anterior axon guidance	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within female gonad development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within gonad morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within male gonad development	ISO Inferred from Sequence Orthology 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
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in system development	IEA Inferred from Electronic Annotation more info

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 homeobox protein 9; LIM-homeodomain type transcription factor 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_181367.2 → NP_852032.1 LIM/homeobox protein Lhx9

See identical proteins and their annotated locations for NP_852032.1

Status: PROVISIONAL

Source sequence(s)

AY273890

UniProtKB/Swiss-Prot

A1A5M2, Q80W90, Q811Z4

UniProtKB/TrEMBL

A0A8I6GJ04

Related

ENSRNOP00000092128.1, ENSRNOT00000101843.2

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

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086031.1 Reference GRCr8

Range

52941207..52961436 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006249919.5 → XP_006249981.1 LIM/homeobox protein Lhx9 isoform X4

See identical proteins and their annotated locations for XP_006249981.1

UniProtKB/TrEMBL

A6ICL2

Related

ENSRNOP00000014218.6, ENSRNOT00000014218.8

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

smart00389
Location:258 → 303

HOX; Homeodomain
XM_006249918.5 → XP_006249980.1 LIM/homeobox protein Lhx9 isoform X3

See identical proteins and their annotated locations for XP_006249980.1

UniProtKB/TrEMBL

A6ICL2

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
XM_006249915.5 → XP_006249977.1 LIM/homeobox protein Lhx9 isoform X2

UniProtKB/TrEMBL

A0A8I6GJ04

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 → 323

Homeobox; Homeobox domain
XM_006249914.5 → XP_006249976.1 LIM/homeobox protein Lhx9 isoform X1

UniProtKB/TrEMBL

A0A8I6GJ04

Related

ENSRNOP00000105014.1, ENSRNOT00000139280.1

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