U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Lhx9 LIM homeobox protein 9 [ Mus musculus (house mouse) ]

Gene ID: 16876, updated on 13-Dec-2022

Summary

Official Symbol
Lhx9provided by MGI
Official Full Name
LIM homeobox protein 9provided by MGI
Primary source
MGI:MGI:1316721
See related
Ensembl:ENSMUSG00000019230 AllianceGenome:MGI:1316721
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
LH2B; 3110009O07Rik
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 cell population proliferation and gonad development. Predicted to be active in nucleus. Is expressed in several structures, including brain; genitourinary system; heart and pericardium; limb; and sensory organ. Orthologous to human LHX9 (LIM homeobox 9). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in whole brain E14.5 (RPKM 7.8), CNS E14 (RPKM 6.5) and 4 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See Lhx9 in Genome Data Viewer
Location:
1; 1 E4
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (138752924..138776577, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (138825186..138848839, complement)

Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene predicted gene 5833 Neighboring gene predicted gene 8790 Neighboring gene RIKEN cDNA 2310009B15 gene Neighboring gene RIKEN cDNA 1700019P21 gene

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (4)  1 citation
  • Endonuclease-mediated (1) 

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

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
PubMed 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001025565.2NP_001020736.1  LIM/homeobox protein Lhx9 isoform a

    See identical proteins and their annotated locations for NP_001020736.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1), also known as Lhx9alpha, represents the longest transcript.
    Source sequence(s)
    AC154398
    Consensus CDS
    CCDS15334.1
    UniProtKB/Swiss-Prot
    Q9WUH2
    UniProtKB/TrEMBL
    A0A6P5Q6H6
    Related
    ENSMUSP00000019374.8, ENSMUST00000019374.14
    Conserved Domains (3) summary
    cd09377
    Location:129187
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:61124
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:271312
    Homeobox; Homeobox domain
  2. NM_001042577.1NP_001036042.1  LIM/homeobox protein Lhx9 isoform c

    See identical proteins and their annotated locations for NP_001036042.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 3' coding region, compared to variant 1. The resulting isoform (c) has a longer, distinct C-terminus that encodes an intact LIM homeodomain, compared to isoform a.
    Source sequence(s)
    AC154398, BC072623
    Consensus CDS
    CCDS35726.1
    UniProtKB/Swiss-Prot
    Q9WU44, Q9WUH2
    UniProtKB/TrEMBL
    A0A8C6IF03
    Related
    ENSMUSP00000107657.3, ENSMUST00000112026.4
    Conserved Domains (3) summary
    cd09377
    Location:129187
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:61124
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:271323
    Homeobox; Homeobox domain
  3. NM_010714.3NP_034844.1  LIM/homeobox protein Lhx9 isoform b

    See identical proteins and their annotated locations for NP_034844.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, 3' UTR, and coding region, compared to variant 1. The resulting isoform (b) maintains the reading frame but is shorter at both the N- and C-termini, compared to isoform a.
    Source sequence(s)
    AB221560, AC144921, AC154398, AJ243851
    Consensus CDS
    CCDS15333.1
    UniProtKB/Swiss-Prot
    Q9WUH2
    UniProtKB/TrEMBL
    A0A6P5Q0Q5, A0A8C6IF65
    Related
    ENSMUSP00000091198.4, ENSMUST00000093486.10
    Conserved Domains (3) summary
    cd09377
    Location:120178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52115
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:258303
    HOX; Homeodomain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000067.7 Reference GRCm39 C57BL/6J

    Range
    138752924..138776577 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036162372.1XP_036018265.1  LIM/homeobox protein Lhx9 isoform X5

    Conserved Domains (3) summary
    cd09377
    Location:119177
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52115
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:257302
    HOX; Homeodomain
  2. XM_036162371.1XP_036018264.1  LIM/homeobox protein Lhx9 isoform X5

    Conserved Domains (3) summary
    cd09377
    Location:119177
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52115
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:257302
    HOX; Homeodomain
  3. XM_030251728.2XP_030107588.1  LIM/homeobox protein Lhx9 isoform X5

    Conserved Domains (3) summary
    cd09377
    Location:119177
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52115
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:257302
    HOX; Homeodomain
  4. XM_036162374.1XP_036018267.1  LIM/homeobox protein Lhx9 isoform X6

    Conserved Domains (3) summary
    cd09377
    Location:110168
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:42105
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:248293
    HOX; Homeodomain
  5. XM_030251703.2XP_030107563.1  LIM/homeobox protein Lhx9 isoform X7

    Conserved Domains (3) summary
    cd09377
    Location:128186
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:61124
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:266311
    HOX; Homeodomain
  6. XM_030251723.1XP_030107583.1  LIM/homeobox protein Lhx9 isoform X4

    UniProtKB/TrEMBL
    A0A6P5Q0Q5, A0A8C6IF65
    Conserved Domains (3) summary
    cd09377
    Location:120178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52115
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:258303
    HOX; Homeodomain
  7. XM_030251724.1XP_030107584.1  LIM/homeobox protein Lhx9 isoform X4

    UniProtKB/TrEMBL
    A0A6P5Q0Q5, A0A8C6IF65
    Conserved Domains (3) summary
    cd09377
    Location:120178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52115
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:258303
    HOX; Homeodomain
  8. XM_030251726.2XP_030107586.1  LIM/homeobox protein Lhx9 isoform X4

    UniProtKB/TrEMBL
    A0A6P5Q0Q5, A0A8C6IF65
    Conserved Domains (3) summary
    cd09377
    Location:120178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52115
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:258303
    HOX; Homeodomain
  9. XM_017318637.2XP_017174126.1  LIM/homeobox protein Lhx9 isoform X4

    UniProtKB/Swiss-Prot
    Q9WUH2
    UniProtKB/TrEMBL
    A0A6P5Q0Q5, A0A8C6IF65
    Conserved Domains (3) summary
    cd09377
    Location:120178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52115
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:258303
    HOX; Homeodomain
  10. XM_006529173.4XP_006529236.1  LIM/homeobox protein Lhx9 isoform X2

    See identical proteins and their annotated locations for XP_006529236.1

    UniProtKB/Swiss-Prot
    Q9WUH2
    Conserved Domains (3) summary
    cd09377
    Location:120178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52115
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:262315
    Homeobox; Homeobox domain
  11. XM_030251701.2XP_030107561.1  LIM/homeobox protein Lhx9 isoform X3

    Conserved Domains (3) summary
    cd09377
    Location:119177
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52115
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:261314
    Homeobox; Homeobox domain
  12. XM_006529172.5XP_006529235.1  LIM/homeobox protein Lhx9 isoform X2

    See identical proteins and their annotated locations for XP_006529235.1

    UniProtKB/Swiss-Prot
    Q9WUH2
    Related
    ENSMUSP00000036480.7, ENSMUST00000046870.13
    Conserved Domains (3) summary
    cd09377
    Location:120178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52115
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:262315
    Homeobox; Homeobox domain
  13. XM_006529171.3XP_006529234.1  LIM/homeobox protein Lhx9 isoform X2

    See identical proteins and their annotated locations for XP_006529234.1

    UniProtKB/Swiss-Prot
    Q9WUH2
    Conserved Domains (3) summary
    cd09377
    Location:120178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52115
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:262315
    Homeobox; Homeobox domain
  14. XM_030251696.1XP_030107556.1  LIM/homeobox protein Lhx9 isoform X2

    Conserved Domains (3) summary
    cd09377
    Location:120178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52115
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:262315
    Homeobox; Homeobox domain
  15. XM_006529170.4XP_006529233.1  LIM/homeobox protein Lhx9 isoform X1

    Conserved Domains (3) summary
    cd09377
    Location:128186
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:61124
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:270323
    Homeobox; Homeobox domain