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    Nr1h5 nuclear receptor subfamily 1, group H, member 5 [ Mus musculus (house mouse) ]

    Gene ID: 381463, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Nr1h5provided by MGI
    Official Full Name
    nuclear receptor subfamily 1, group H, member 5provided by MGI
    Primary source
    MGI:MGI:3026618
    See related
    Ensembl:ENSMUSG00000048938 AllianceGenome:MGI:3026618
    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
    Fxrb
    Summary
    Predicted to enable RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and nuclear receptor activity. Predicted to be involved in cell differentiation; negative regulation of inflammatory response; and regulation of transcription by RNA polymerase II. Predicted to be part of RNA polymerase II transcription regulator complex. Predicted to be active in nucleus. Orthologous to human NR1H5P (nuclear receptor subfamily 1 group H member 5, pseudogene). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in liver E14 (RPKM 3.1), liver E14.5 (RPKM 2.8) and 5 other tissues See more
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    Genomic context

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    See Nr1h5 in Genome Data Viewer
    Location:
    3 F2.2; 3 45.25 cM
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (102846974..102871607, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (102939658..102964291, complement)

    Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer mm9_chr3:102608013-102608314 Neighboring gene thyroid stimulating hormone, beta subunit Neighboring gene synaptonemal complex protein 1 Neighboring gene STARR-seq mESC enhancer starr_08580 Neighboring gene predicted gene, 33866 Neighboring gene STARR-positive B cell enhancer ABC_E11206 Neighboring gene predicted gene, 22826 Neighboring gene STARR-positive B cell enhancer ABC_E4568 Neighboring gene STARR-seq mESC enhancer starr_08583 Neighboring gene suppressor of IKBKE 1 Neighboring gene cold shock domain containing E1, RNA binding Neighboring gene STARR-seq mESC enhancer starr_08584

    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. Identification of farnesoid X receptor beta as a novel mammalian nuclear receptor sensing lanosterol. Otte K, et al. Mol Cell Biol, 2003 Feb. PMID 12529392, Free PMC Article
    2. Large tumor suppressor homologs 1 and 2 regulate mouse liver progenitor cell proliferation and maturation through antagonism of the coactivators YAP and TAZ. Yi J, et al. Hepatology, 2016 Nov. PMID 27531557, Free PMC Article
    3. A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain. Thompson CL, et al. Neuron, 2014 Jul 16. PMID 24952961, Free PMC Article
    4. Genetic determinants of micronucleus formation in vivo. Adams DJ, et al. Nature, 2024 Mar. PMID 38355793, Free PMC Article
    5. A high-resolution anatomical atlas of the transcriptome in the mouse embryo. Diez-Roux G, et al. PLoS Biol, 2011 Jan 18. PMID 21267068, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

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

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC141184

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nuclear receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in bile acid signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of inflammatory response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    nuclear receptor subfamily 1, group H, member 5

    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_198658.2 → NP_941060.2  nuclear receptor subfamily 1, group H, member 5 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC122219
      Consensus CDS
      CCDS38568.1
      UniProtKB/TrEMBL
      E9Q5A6, Q80ST6
      Related
      ENSMUSP00000052557.9, ENSMUST00000058899.13
      Conserved Domains (2) summary
      cd06962
      Location:119 → 202
      NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
      cl11397
      Location:247 → 497
      NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators

    2. NM_201619.2 → NP_963913.2  nuclear receptor subfamily 1, group H, member 5 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC122219
      Consensus CDS
      CCDS79988.1
      UniProtKB/TrEMBL
      A0A0G2JEJ9, Q811X2
      Related
      ENSMUSP00000142799.2, ENSMUST00000196983.5
      Conserved Domains (2) summary
      cd06962
      Location:119 → 202
      NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
      cl11397
      Location:247 → 489
      NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators

    3. NM_201622.2 → NP_963916.2  nuclear receptor subfamily 1, group H, member 5 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC122219
      Consensus CDS
      CCDS79989.1
      UniProtKB/TrEMBL
      A0A0G2JG67, Q811W9
      Related
      ENSMUSP00000143445.2, ENSMUST00000196135.2
      Conserved Domains (2) summary
      cl02596
      Location:86 → 144
      NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
      cl11397
      Location:189 → 439
      NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators

    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_000069.7 Reference GRCm39 C57BL/6J

      Range
      102846974..102871607 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006501623.4 → XP_006501686.1  nuclear receptor subfamily 1, group H, member 5 isoform X1

      UniProtKB/TrEMBL
      Q80ST6
      Conserved Domains (2) summary
      cd06936
      Location:335 → 585
      NR_LBD_Fxr; The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors
      cd06962
      Location:207 → 290
      NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers

    2. XM_006501626.4 → XP_006501689.1  nuclear receptor subfamily 1, group H, member 5 isoform X4

      UniProtKB/TrEMBL
      Q811W9
      Conserved Domains (2) summary
      cl02596
      Location:22 → 80
      NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
      cl11397
      Location:125 → 375
      NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators

    3. XM_011240153.1 → XP_011238455.1  nuclear receptor subfamily 1, group H, member 5 isoform X3

      UniProtKB/TrEMBL
      Q80ST6
      Conserved Domains (2) summary
      cd06962
      Location:87 → 170
      NR_DBD_FXR; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers
      cl11397
      Location:215 → 465
      NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators

    4. XM_006501624.4 → XP_006501687.1  nuclear receptor subfamily 1, group H, member 5 isoform X2

      UniProtKB/TrEMBL
      Q80ST6
      Conserved Domains (2) summary
      cl02596
      Location:93 → 176
      NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
      cl11397
      Location:221 → 471
      NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators

    RNA

    1. XR_375534.4 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_201620.1: Suppressed sequence

      Description
      NM_201620.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

    2. NM_201621.1: Suppressed sequence

      Description
      NM_201621.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein Strain
    Heading Accession and Version

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