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    Xlr4b X-linked lymphocyte-regulated 4B [ Mus musculus (house mouse) ]

    Gene ID: 27083, updated on 8-Feb-2024

    Summary

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    Official Symbol
    Xlr4bprovided by MGI
    Official Full Name
    X-linked lymphocyte-regulated 4Bprovided by MGI
    Primary source
    MGI:MGI:1350975
    See related
    Ensembl:ENSMUSG00000067768 AllianceGenome:MGI:1350975
    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
    Xlr4
    Summary
    Involved in positive regulation of dendritic spine morphogenesis and positive regulation of synapse assembly. Predicted to be located in nucleoplasm. Predicted to be active in synaptonemal complex. Is expressed in brain; hindgut diverticulum; liver; placenta; and yolk sac. Orthologous to human FAM9B (family with sequence similarity 9 member B) and FAM9C (family with sequence similarity 9 member C). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in placenta adult (RPKM 20.5), thymus adult (RPKM 4.3) and 2 other tissues See more
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    Genomic context

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    See Xlr4b in Genome Data Viewer
    Location:
    X A7.3; X 37.29 cM
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (72257928..72266059)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (73214321..73222453)

    Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_47343 Neighboring gene spindlin family, member 2D Neighboring gene STARR-seq mESC enhancer starr_47344 Neighboring gene X-linked lymphocyte-regulated 3B Neighboring gene factor 8-associated gene A Neighboring gene X-linked lymphocyte-regulated 4C

    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. Xlr4 as a new candidate gene underlying vulnerability to cocaine effects. Di Segni M, et al. Neuropharmacology, 2020 May 15. PMID 32113966
    2. Cux1 and Cux2 regulate dendritic branching, spine morphology, and synapses of the upper layer neurons of the cortex. Cubelos B, et al. Neuron, 2010 May 27. PMID 20510857, Free PMC Article
    3. At Term, XmO and XpO Mouse Placentas Show Differences in Glucose Metabolism in the Trophectoderm-Derived Outer Zone. He N, et al. Front Cell Dev Biol, 2017. PMID 28680878, Free PMC Article
    4. Xlr3b is a new imprinted candidate for X-linked parent-of-origin effects on cognitive function in mice. Davies W, et al. Nat Genet, 2005 Jun. PMID 15908950
    5. Identification of a cluster of X-linked imprinted genes in mice. Raefski AS, et al. Nat Genet, 2005 Jun. PMID 15908953

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within dendritic spine organization IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within dopamine secretion IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in meiotic cell cycle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of dendritic spine morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of synapse assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to cocaine IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in spermatid development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in synaptonemal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    X-linked lymphocyte-regulated 4B
    Names
    X-linked lymphocyte regulated gene 4

    NCBI Reference Sequences (RefSeq)

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    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_001293676.1 → NP_001280605.1  X-linked lymphocyte-regulated 4B

      See identical proteins and their annotated locations for NP_001280605.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1, 2, 3, 4, 5, and 6 encode the same protein.
      Source sequence(s)
      BC034848, BE627633, BU755708, BX571735
      Consensus CDS
      CCDS41010.1
      UniProtKB/TrEMBL
      Q9JJQ7, Q9JJQ8
      Related
      ENSMUSP00000116105.2, ENSMUST00000156188.8
      Conserved Domains (1) summary
      pfam04803
      Location:60 → 188
      Cor1; Cor1/Xlr/Xmr conserved region

    2. NM_001293677.1 → NP_001280606.1  X-linked lymphocyte-regulated 4B

      See identical proteins and their annotated locations for NP_001280606.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1, 2, 3, 4, 5, and 6 encode the same protein.
      Source sequence(s)
      BC034848, BE627633, BU755708, BX571735
      Consensus CDS
      CCDS41010.1
      UniProtKB/TrEMBL
      Q9JJQ7, Q9JJQ8
      Conserved Domains (1) summary
      pfam04803
      Location:60 → 188
      Cor1; Cor1/Xlr/Xmr conserved region

    3. NM_001293678.1 → NP_001280607.1  X-linked lymphocyte-regulated 4B

      See identical proteins and their annotated locations for NP_001280607.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, compared to variant 1. Variants 1, 2, 3, 4, 5, and 6 encode the same protein.
      Source sequence(s)
      BC034848, BE627633, BU755708, BX571735
      Consensus CDS
      CCDS41010.1
      UniProtKB/TrEMBL
      Q9JJQ7, Q9JJQ8
      Conserved Domains (1) summary
      pfam04803
      Location:60 → 188
      Cor1; Cor1/Xlr/Xmr conserved region

    4. NM_001293679.1 → NP_001280608.1  X-linked lymphocyte-regulated 4B

      See identical proteins and their annotated locations for NP_001280608.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, compared to variant 1. Variants 1, 2, 3, 4, 5, and 6 encode the same protein.
      Source sequence(s)
      BC034848, BE627633, BU755708, BX571735
      Consensus CDS
      CCDS41010.1
      UniProtKB/TrEMBL
      Q9JJQ7, Q9JJQ8
      Conserved Domains (1) summary
      pfam04803
      Location:60 → 188
      Cor1; Cor1/Xlr/Xmr conserved region

    5. NM_001293680.1 → NP_001280609.1  X-linked lymphocyte-regulated 4B

      See identical proteins and their annotated locations for NP_001280609.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR, compared to variant 1. Variants 1, 2, 3, 4, 5, and 6 encode the same protein.
      Source sequence(s)
      BC034848, BE627633, BU755708, BX571735
      Consensus CDS
      CCDS41010.1
      UniProtKB/TrEMBL
      Q9JJQ7, Q9JJQ8
      Related
      ENSMUSP00000064686.4, ENSMUST00000069077.10
      Conserved Domains (1) summary
      pfam04803
      Location:60 → 188
      Cor1; Cor1/Xlr/Xmr conserved region

    6. NM_021365.3 → NP_067340.2  X-linked lymphocyte-regulated 4B

      See identical proteins and their annotated locations for NP_067340.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, 3, 4, 5, and 6 encode the same protein.
      Source sequence(s)
      BC034848, BE627633, BU755708, BX571735
      Consensus CDS
      CCDS41010.1
      UniProtKB/TrEMBL
      Q9JJQ7, Q9JJQ8
      Related
      ENSMUSP00000066171.5, ENSMUST00000069103.11
      Conserved Domains (1) summary
      pfam04803
      Location:60 → 188
      Cor1; Cor1/Xlr/Xmr conserved region

    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_000086.8 Reference GRCm39 C57BL/6J

      Range
      72257928..72266059
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011247605.3 → XP_011245907.1  X-linked lymphocyte-regulated 4B isoform X1

      See identical proteins and their annotated locations for XP_011245907.1

      UniProtKB/TrEMBL
      Q9JJQ7, Q9JJQ8
      Conserved Domains (1) summary
      pfam04803
      Location:60 → 188
      Cor1; Cor1/Xlr/Xmr conserved region

    2. XM_006528061.4 → XP_006528124.1  X-linked lymphocyte-regulated 4B isoform X1

      See identical proteins and their annotated locations for XP_006528124.1

      UniProtKB/TrEMBL
      Q9JJQ7, Q9JJQ8
      Related
      ENSMUSP00000080511.4, ENSMUST00000081827.4
      Conserved Domains (1) summary
      pfam04803
      Location:60 → 188
      Cor1; Cor1/Xlr/Xmr conserved region

    3. XM_011247606.3 → XP_011245908.1  X-linked lymphocyte-regulated 4B isoform X1

      See identical proteins and their annotated locations for XP_011245908.1

      UniProtKB/TrEMBL
      Q9JJQ7, Q9JJQ8
      Conserved Domains (1) summary
      pfam04803
      Location:60 → 188
      Cor1; Cor1/Xlr/Xmr conserved region

    4. XM_011247604.3 → XP_011245906.1  X-linked lymphocyte-regulated 4B isoform X1

      See identical proteins and their annotated locations for XP_011245906.1

      UniProtKB/TrEMBL
      Q9JJQ7, Q9JJQ8
      Conserved Domains (1) summary
      pfam04803
      Location:60 → 188
      Cor1; Cor1/Xlr/Xmr conserved region
    Nucleotide Protein Strain
    Heading Accession and Version

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