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    Lmbr1 limb region 1 [ Mus musculus (house mouse) ]

    Gene ID: 56873, updated on 9-May-2024

    Summary

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    Official Symbol
    Lmbr1provided by MGI
    Official Full Name
    limb region 1provided by MGI
    Primary source
    MGI:MGI:1861746
    See related
    Ensembl:ENSMUSG00000010721 AllianceGenome:MGI:1861746
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    1110048D14Rik
    Summary
    This gene encodes a member of the LMBR1-like membrane protein family. Another member of this protein family has been shown to be a lipocalin transmembrane receptor. A highly conserved, cis-acting regulatory module for the sonic hedgehog gene is located within an intron of this gene. Consequently, disruption of this genic region can alter sonic hedgehog expression and affect limb patterning, but it is not known if this gene functions directly in limb development. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis adult (RPKM 2.4), CNS E18 (RPKM 2.2) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    5 B1; 5
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (29434800..29583414, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (29229802..29378421, complement)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_12726 Neighboring gene predicted gene, 35881 Neighboring gene mammal reptile conserved sequence 1 Neighboring gene STARR-seq mESC enhancer starr_12727 Neighboring gene STARR-seq mESC enhancer starr_12728 Neighboring gene mammal fish conserved sequence 3 Neighboring gene STARR-seq mESC enhancer starr_12729 Neighboring gene mammal fish conserved sequence 4 Neighboring gene ring finger protein 32 Neighboring gene predicted gene 7420 Neighboring gene mammal amphibian conserved sequence 1 Neighboring gene STARR-seq mESC enhancer starr_12732 Neighboring gene STARR-seq mESC enhancer starr_12733 Neighboring gene STARR-seq mESC enhancer starr_12734 Neighboring gene zone of polarising activity regulatory sequence 1 Neighboring gene STARR-positive B cell enhancer ABC_E9634 Neighboring gene predicted gene, 36086 Neighboring gene STARR-positive B cell enhancer ABC_E9252 Neighboring gene nucleolar protein with MIF4G domain 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Disruption of the C7orf2/Lmbr1 genic region is associated with preaxial polydactyly in humans and mice. Horikoshi T, et al. J Bone Miner Metab, 2003. PMID 12491086
    2. Reciprocal mouse and human limb phenotypes caused by gain- and loss-of-function mutations affecting Lmbr1. Clark RM, et al. Genetics, 2001 Oct. PMID 11606546, Free PMC Article
    3. Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia. Ushiki A, et al. Nat Commun, 2021 Apr 16. PMID 33863876, Free PMC Article
    4. Developmentally regulated Shh expression is robust to TAD perturbations. Williamson I, et al. Development, 2019 Sep 30. PMID 31511252, Free PMC Article
    5. The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances. Symmons O, et al. Dev Cell, 2016 Dec 5. PMID 27867070, Free PMC Article

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. disruption is associated with preaxial polydactyly
      Title: Disruption of the C7orf2/Lmbr1 genic region is associated with preaxial polydactyly in humans and mice.
    2. intron 5 sequence of the Lmbr1 locus contains a major limb-specific sonic hedgehog enhancer that is necessary for distal limb development
      Title: Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables transmembrane signaling receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within embryonic digit morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within embryonic hindlimb morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    limb region 1 protein

    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_020295.3 → NP_064691.2  limb region 1 protein

      See identical proteins and their annotated locations for NP_064691.2

      Status: REVIEWED

      Source sequence(s)
      AC159298, AK030631, AK195974, BB614787, BM898643
      Consensus CDS
      CCDS19148.1
      UniProtKB/Swiss-Prot
      Q766D0, Q91WC6, Q9JIS9, Q9JIT0
      UniProtKB/TrEMBL
      J3QM78
      Related
      ENSMUSP00000058405.5, ENSMUST00000055195.11
      Conserved Domains (1) summary
      pfam04791
      Location:26 → 445
      LMBR1; LMBR1-like membrane protein

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000071.7 Reference GRCm39 C57BL/6J

      Range
      29434800..29583414 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006535767.5 → XP_006535830.1  limb region 1 protein isoform X4

      UniProtKB/TrEMBL
      J3QM78
      Conserved Domains (1) summary
      pfam04791
      Location:66 → 331
      LMBR1; LMBR1-like membrane protein

    2. XM_006535765.5 → XP_006535828.1  limb region 1 protein isoform X2

      See identical proteins and their annotated locations for XP_006535828.1

      UniProtKB/TrEMBL
      J3QM78
      Conserved Domains (1) summary
      pfam04791
      Location:12 → 414
      LMBR1; LMBR1-like membrane protein

    3. XM_006535764.5 → XP_006535827.1  limb region 1 protein isoform X1

      UniProtKB/TrEMBL
      J3QM78
      Related
      ENSMUSP00000142755.2, ENSMUST00000198105.5
      Conserved Domains (1) summary
      pfam04791
      Location:19 → 444
      LMBR1; LMBR1-like membrane protein

    4. XM_011249782.4 → XP_011248084.1  limb region 1 protein isoform X2

      See identical proteins and their annotated locations for XP_011248084.1

      UniProtKB/TrEMBL
      J3QM78
      Conserved Domains (1) summary
      pfam04791
      Location:12 → 414
      LMBR1; LMBR1-like membrane protein

    5. XM_006535768.5 → XP_006535831.1  limb region 1 protein isoform X5

      See identical proteins and their annotated locations for XP_006535831.1

      UniProtKB/TrEMBL
      A0A0G2JFU9, A0A0G2JFX9
      Related
      ENSMUSP00000143348.2, ENSMUST00000196321.5
      Conserved Domains (1) summary
      pfam04791
      Location:1 → 327
      LMBR1; LMBR1-like membrane protein

    6. XM_006535770.5 → XP_006535833.1  limb region 1 protein isoform X6

      UniProtKB/TrEMBL
      A0A0G2JFU9
      Conserved Domains (1) summary
      pfam04791
      Location:50 → 315
      LMBR1; LMBR1-like membrane protein

    7. XM_030254722.2 → XP_030110582.1  limb region 1 protein isoform X6

      UniProtKB/TrEMBL
      A0A0G2JFU9
      Conserved Domains (1) summary
      pfam04791
      Location:50 → 315
      LMBR1; LMBR1-like membrane protein

    8. XM_036165361.1 → XP_036021254.1  limb region 1 protein isoform X3

      UniProtKB/TrEMBL
      J3QM78
      Conserved Domains (1) summary
      pfam04791
      Location:19 → 412
      LMBR1; LMBR1-like membrane protein

    9. XM_006535771.5 → XP_006535834.1  limb region 1 protein isoform X7

      Conserved Domains (1) summary
      pfam04791
      Location:19 → 253
      LMBR1; LMBR1-like membrane protein

    10. XM_006535772.5 → XP_006535835.1  limb region 1 protein isoform X8

      Conserved Domains (1) summary
      pfam04791
      Location:19 → 251
      LMBR1; LMBR1-like membrane protein

    RNA

    1. XR_004942544.1 RNA Sequence

    2. XR_004942545.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9JIT0.1 GenPept UniProtKB/Swiss-Prot:Q9JIT0

    Gene LinkOut

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

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