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

Gene ID: 289048, updated on 27-Nov-2024

Summary

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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, Nov 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

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See Lhx9 in Genome Data Viewer
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_086031.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134481500 Neighboring gene prothymosin alpha, pseudogene 4 Neighboring gene uncharacterized LOC108352542 Neighboring gene uncharacterized LOC134481501 Neighboring gene similar to human chromosome 1 open reading frame 53 Neighboring gene uncharacterized LOC120096262

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: 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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Related articles in PubMed

  1. Lhx9 and lhx9alpha: differential biochemical properties and effects on neuronal differentiation. Mollé B, et al. DNA Cell Biol, 2004 Nov. PMID 15585134
  2. Lhx9 expression during gonadal morphogenesis as related to the state of cell differentiation. Mazaud S, et al. Gene Expr Patterns, 2002 Dec. PMID 12617828
  3. The LIM homeobox gene Lhx9 is essential for mouse gonad formation. Birk OS, et al. Nature, 2000 Feb 24. PMID 10706291
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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

Homology

Clone Names

  • MGC156570

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)

  1. 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

  1. NC_086031.1 Reference GRCr8

    Range
    52941207..52961436 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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

  3. 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

  4. 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
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q80W90.1 GenPept UniProtKB/Swiss-Prot:Q80W90

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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