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Lhx1 LIM homeobox 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 257634, updated on 2-Nov-2024

Summary

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Official Symbol: Lhx1provided by RGD
Official Full Name: LIM homeobox 1provided by RGD
Primary source: RGD:71074
See related: EnsemblRapid:ENSRNOG00000002812 AllianceGenome:RGD:71074
Gene type: protein coding
RefSeq status: VALIDATED
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; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and cis-regulatory region sequence-specific DNA binding activity. Involved in cellular response to fibroblast growth factor stimulus and kidney development. Located in nucleus. Orthologous to human LHX1 (LIM homeobox 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Kidney (RPKM 36.3) and Brain (RPKM 15.7) See more
Orthologs: human mouse all
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Genomic context

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See Lhx1 in Genome Data Viewer

Location:: 10q26

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (69894288..69901076, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (69396829..69403617, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (71843991..71849293, complement)

Chromosome 10 - NC_086028.1 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

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

General gene information

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Markers

Lhx1 (e-PCR), detects polymorphism
- UniSTS:178184

Lhx1 (e-PCR), detects polymorphism
- UniSTS:507019

D10Rat90 (e-PCR)
- UniSTS:118216

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in S-shaped body morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in S-shaped body morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within anatomical structure formation involved in morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in anatomical structure formation involved in morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within anatomical structure morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in anatomical structure morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within anterior/posterior axis specification	ISO Inferred from Sequence Orthology more info
involved_in anterior/posterior axis specification	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within anterior/posterior pattern specification	ISO Inferred from Sequence Orthology more info
involved_in anterior/posterior pattern specification	ISS Inferred from Sequence or Structural Similarity more info
involved_in branching involved in ureteric bud morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell-cell signaling	ISO Inferred from Sequence Orthology more info
involved_in cell-cell signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to fibroblast growth factor stimulus	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within cerebellar Purkinje cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in cerebellar Purkinje cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within cerebellum development	ISO Inferred from Sequence Orthology more info
involved_in cerebellum development	ISS Inferred from Sequence or Structural Similarity more info
involved_in cervix development	ISO Inferred from Sequence Orthology more info
involved_in cervix development	ISS Inferred from Sequence or Structural Similarity more info
involved_in comma-shaped body morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in comma-shaped body morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within dorsal/ventral pattern formation	ISO Inferred from Sequence Orthology more info
involved_in dorsal/ventral pattern formation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within ectoderm formation	ISO Inferred from Sequence Orthology more info
involved_in ectoderm formation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within embryonic pattern specification	ISO Inferred from Sequence Orthology more info
involved_in embryonic pattern specification	ISS Inferred from Sequence or Structural Similarity more info
involved_in embryonic retina morphogenesis in camera-type eye	ISO Inferred from Sequence Orthology more info
involved_in embryonic retina morphogenesis in camera-type eye	ISS Inferred from Sequence or Structural Similarity more info
involved_in embryonic viscerocranium morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in embryonic viscerocranium morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within endoderm development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within endoderm formation	ISO Inferred from Sequence Orthology more info
involved_in endoderm formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in epithelium development	ISO Inferred from Sequence Orthology more info
involved_in epithelium development	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within forebrain regionalization	ISO Inferred from Sequence Orthology more info
involved_in forebrain regionalization	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within gastrulation with mouth forming second	ISO Inferred from Sequence Orthology more info
involved_in gastrulation with mouth forming second	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within head development	ISO Inferred from Sequence Orthology more info
involved_in head development	ISO Inferred from Sequence Orthology more info
involved_in head development	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within kidney development	ISO Inferred from Sequence Orthology more info
involved_in kidney development	ISS Inferred from Sequence or Structural Similarity more info
involved_in lateral motor column neuron migration	ISO Inferred from Sequence Orthology more info
involved_in lateral motor column neuron migration	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of mesendoderm development	ISO Inferred from Sequence Orthology more info
involved_in mesonephric duct development	IEP Inferred from Expression Pattern more info	PubMed
involved_in mesonephric tubule development	IEP Inferred from Expression Pattern more info	PubMed
involved_in mesonephros development	ISO Inferred from Sequence Orthology more info
involved_in metanephric S-shaped body morphogenesis	IEP Inferred from Expression Pattern more info	PubMed
involved_in metanephric S-shaped body morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in metanephric comma-shaped body morphogenesis	IEP Inferred from Expression Pattern more info	PubMed
involved_in metanephric glomerulus development	IEP Inferred from Expression Pattern more info	PubMed
involved_in metanephric part of ureteric bud development	IEP Inferred from Expression Pattern more info	PubMed
involved_in metanephric renal vesicle morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in metanephros development	ISO Inferred from Sequence Orthology more info
involved_in motor neuron axon guidance	ISO Inferred from Sequence Orthology more info
involved_in motor neuron axon guidance	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of DNA-templated transcription	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 nephric duct elongation	ISO Inferred from Sequence Orthology more info
involved_in nephric duct morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in nephric duct morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in oviduct development	ISO Inferred from Sequence Orthology more info
involved_in oviduct development	ISS Inferred from Sequence or Structural Similarity more info
involved_in oviduct epithelium development	ISO Inferred from Sequence Orthology more info
involved_in oviduct epithelium development	ISS Inferred from Sequence or Structural Similarity more info
involved_in paramesonephric duct development	ISO Inferred from Sequence Orthology more info
involved_in paramesonephric duct development	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within pattern specification process	ISO Inferred from Sequence Orthology more info
involved_in pattern specification process	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of anterior head development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of anterior head development	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of branching involved in ureteric bud morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of branching involved in ureteric bud morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of embryonic development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of embryonic development	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of gastrulation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gastrulation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of nephron tubule epithelial cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of nephron tubule epithelial cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within post-embryonic development	ISO Inferred from Sequence Orthology more info
involved_in post-embryonic development	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within primitive streak formation	ISO Inferred from Sequence Orthology more info
involved_in primitive streak formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in pronephros development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in renal vesicle morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in renal vesicle morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in retina development in camera-type eye	ISO Inferred from Sequence Orthology more info
involved_in retina layer formation	ISO Inferred from Sequence Orthology more info
involved_in retina layer formation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within somite rostral/caudal axis specification	ISO Inferred from Sequence Orthology more info
involved_in spinal cord association neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in spinal cord association neuron differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in spinal cord development	ISO Inferred from Sequence Orthology more info
involved_in telencephalon development	ISO Inferred from Sequence Orthology more info
involved_in transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within ureter morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ureteric bud development	ISO Inferred from Sequence Orthology more info
involved_in ureteric bud development	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within urogenital system development	ISO Inferred from Sequence Orthology more info
involved_in urogenital system development	ISS Inferred from Sequence or Structural Similarity more info
involved_in uterine epithelium development	ISO Inferred from Sequence Orthology more info
involved_in uterine epithelium development	ISS Inferred from Sequence or Structural Similarity more info
involved_in uterus development	ISO Inferred from Sequence Orthology more info
involved_in uterus development	ISS Inferred from Sequence or Structural Similarity more info
involved_in vagina development	ISO Inferred from Sequence Orthology more info
involved_in vagina development	ISS Inferred from Sequence or Structural Similarity more info
involved_in ventral spinal cord development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	ISS Inferred from Sequence or Structural Similarity more info
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: LIM/homeobox protein Lhx1

Names: LIM homeobox protein 1; homeobox protein Lim-1; rlim

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_145880.4 → NP_665887.3 LIM/homeobox protein Lhx1

See identical proteins and their annotated locations for NP_665887.3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/Swiss-Prot

P63007

UniProtKB/TrEMBL

A6HHL1

Related

ENSRNOP00000003799.2, ENSRNOT00000003799.5

Conserved Domains (4) summary

cd09367
Location:4 → 55

LIM1_Lhx1_Lhx5; The first LIM domain of Lhx1 (also known as Lim1) and Lhx5

cd09375
Location:63 → 118

LIM2_Lhx1_Lhx5; The second LIM domain of Lhx1 (also known as Lim1) and Lhx5

PRK14086
Location:263 → 382

dnaA; chromosomal replication initiator protein DnaA

pfam00046
Location:183 → 237

Homeobox; Homeobox domain