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    Lnx1 ligand of numb-protein X 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 360926, updated on 2-Nov-2024

    Summary

    Official Symbol
    Lnx1provided by RGD
    Official Full Name
    ligand of numb-protein X 1provided by RGD
    Primary source
    RGD:1308159
    See related
    EnsemblRapid:ENSRNOG00000002272 AllianceGenome:RGD:1308159
    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 PDZ domain binding activity; identical protein binding activity; and ubiquitin-protein transferase activity. Predicted to be involved in synapse maturation and ubiquitin-dependent protein catabolic process. Predicted to be active in cytoplasm; hippocampal mossy fiber to CA3 synapse; and postsynapse. Orthologous to human LNX1 (ligand of numb-protein X 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Heart (RPKM 81.6), Kidney (RPKM 42.0) and 9 other tissues See more
    Orthologs
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    Genomic context

    See Lnx1 in Genome Data Viewer
    Location:
    14p11
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 14 NC_086032.1 (33868517..33971217)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 14 NC_051349.1 (33514429..33617086)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 14 NC_005113.4 (36047136..36149740)

    Chromosome 14 - NC_086032.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120096595 Neighboring gene uncharacterized LOC134481742 Neighboring gene uncharacterized LOC134481839 Neighboring gene factor interacting with PAPOLA and CPSF1 Neighboring gene sec1 family domain containing 2 Neighboring gene U6 spliceosomal RNA Neighboring gene RAS-like family 11 member B

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables PDZ domain binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables ubiquitin-protein transferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ubiquitin-protein transferase activity ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    involved_in synapse maturation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within ubiquitin-dependent protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in hippocampal mossy fiber to CA3 synapse ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in postsynapse ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    E3 ubiquitin-protein ligase LNX
    Names
    ligand of numb-protein X 1, E3 ubiquitin protein ligase
    NP_001101828.1
    XP_006250964.1
    XP_006250965.1
    XP_006250966.1
    XP_038948102.1

    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_001108358.1NP_001101828.1  E3 ubiquitin-protein ligase LNX

      See identical proteins and their annotated locations for NP_001101828.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473981
      UniProtKB/TrEMBL
      B6RHI5, B6RHI6, F7EWI3
      Related
      ENSRNOP00000003088.3, ENSRNOT00000003088.7
      Conserved Domains (3) summary
      smart00184
      Location:4581
      RING; Ring finger
      COG0265
      Location:260364
      DegQ; Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
      cd00992
      Location:637721
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

    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_086032.1 Reference GRCr8

      Range
      33868517..33971217
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039092174.2XP_038948102.1  E3 ubiquitin-protein ligase LNX isoform X4

      UniProtKB/TrEMBL
      A0A8I5ZXC4
      Conserved Domains (2) summary
      cd00992
      Location:276360
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cd16779
      Location:4283
      mRING-HC-C3HC3D_LNX1; Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1)
    2. XM_006250902.5XP_006250964.1  E3 ubiquitin-protein ligase LNX isoform X1

      UniProtKB/TrEMBL
      B6RHI5
      Conserved Domains (2) summary
      smart00184
      Location:4581
      RING; Ring finger
      cd00992
      Location:627711
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    3. XM_006250903.5XP_006250965.1  E3 ubiquitin-protein ligase LNX isoform X2

      See identical proteins and their annotated locations for XP_006250965.1

      UniProtKB/TrEMBL
      A0A0G2JUI7, A6JD15, B6RHI7
      Related
      ENSRNOP00000069112.1, ENSRNOT00000082183.3
      Conserved Domains (1) summary
      cd00992
      Location:537621
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    4. XM_006250904.5XP_006250966.1  E3 ubiquitin-protein ligase LNX isoform X3

      UniProtKB/TrEMBL
      B6RHI7
      Conserved Domains (1) summary
      cd00992
      Location:527611
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...