U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Protein

    • Showing Current items.

    Pdlim4 PDZ and LIM domain 4 [ Mus musculus (house mouse) ]

    Gene ID: 30794, updated on 27-Nov-2024

    Summary

    Official Symbol
    Pdlim4provided by MGI
    Official Full Name
    PDZ and LIM domain 4provided by MGI
    Primary source
    MGI:MGI:1353470
    See related
    Ensembl:ENSMUSG00000020388 AllianceGenome:MGI:1353470
    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
    Ril
    Summary
    Enables protein phosphatase binding activity. Predicted to be involved in several processes, including actin cytoskeleton organization; excitatory chemical synaptic transmission; and positive regulation of stress fiber assembly. Predicted to be located in several cellular components, including endosome lumen; lamellipodium; and postsynaptic membrane. Predicted to be part of filamentous actin. Predicted to be active in Z disc; adherens junction; and stress fiber. Is expressed in several structures, including alimentary system; central nervous system; embryo mesenchyme; genitourinary system; and sensory organ. Human ortholog(s) of this gene implicated in osteoporosis. Orthologous to human PDLIM4 (PDZ and LIM domain 4). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in ovary adult (RPKM 165.2), stomach adult (RPKM 74.2) and 17 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Pdlim4 in Genome Data Viewer
    Location:
    11 B1.3; 11 32.13 cM
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (53945754..53959814, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (54054928..54069032, complement)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene solute carrier family 22 (organic cation transporter), member 21 Neighboring gene predicted gene 12219 Neighboring gene predicted gene, 30927 Neighboring gene solute carrier family 22 (organic cation transporter), member 4 Neighboring gene VISTA enhancer mm51 Neighboring gene STARR-positive B cell enhancer mm9_chr11:53905235-53905536 Neighboring gene procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha II polypeptide Neighboring gene STARR-positive B cell enhancer mm9_chr11:53953540-53953841 Neighboring gene STARR-positive B cell enhancer ABC_E196 Neighboring gene predicted gene 12223 Neighboring gene TBCC domain containing 1 pseudogene

    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

    Variation

    Alleles

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables actin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables actinin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables alpha-actinin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables alpha-actinin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables muscle alpha-actinin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein phosphatase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein phosphatase binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    involved_in actin cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in actin cytoskeleton organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in actin cytoskeleton organization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in excitatory chemical synaptic transmission ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in excitatory chemical synaptic transmission ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in heart development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in muscle structure development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of stress fiber assembly ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    is_active_in Z disc IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in actin cytoskeleton ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoskeleton ISO
    Inferred from Sequence Orthology
    more info
     
    located_in dendritic spine ISO
    Inferred from Sequence Orthology
    more info
     
    located_in dendritic spine ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in early endosome lumen ISO
    Inferred from Sequence Orthology
    more info
     
    located_in early endosome lumen ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    part_of filamentous actin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of filamentous actin IEA
    Inferred from Electronic Annotation
    more info
     
    part_of filamentous actin ISO
    Inferred from Sequence Orthology
    more info
     
    located_in lamellipodium IEA
    Inferred from Electronic Annotation
    more info
     
    located_in lamellipodium ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in postsynaptic membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in postsynaptic membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in recycling endosome lumen ISO
    Inferred from Sequence Orthology
    more info
     
    located_in recycling endosome lumen ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in recycling endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in stress fiber IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in stress fiber IEA
    Inferred from Electronic Annotation
    more info
     
    located_in stress fiber ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    PDZ and LIM domain protein 4
    Names
    LIM protein RIL
    reversion induced LIM
    reversion-induced LIM protein

    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_001425512.1NP_001412441.1  PDZ and LIM domain protein 4 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL596444
    2. NM_001425513.1NP_001412442.1  PDZ and LIM domain protein 4 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL596444
    3. NM_001425514.1NP_001412443.1  PDZ and LIM domain protein 4 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL596444
      UniProtKB/TrEMBL
      Q5SWV3
      Related
      ENSMUSP00000090797.5, ENSMUST00000093109.11
    4. NM_001425515.1NP_001412444.1  PDZ and LIM domain protein 4 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL596444
    5. NM_019417.4NP_062290.2  PDZ and LIM domain protein 4 isoform 1

      See identical proteins and their annotated locations for NP_062290.2

      Status: VALIDATED

      Source sequence(s)
      AL596444
      Consensus CDS
      CCDS24690.1
      UniProtKB/Swiss-Prot
      P70271, Q5SWV2, Q8K0W4
      Related
      ENSMUSP00000018755.4, ENSMUST00000018755.10
      Conserved Domains (3) summary
      cd09451
      Location:255307
      LIM_RIL; The LIM domain of RIL
      cd00992
      Location:280
      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) ...
      pfam15936
      Location:150226
      DUF4749; Domain of unknown function (DUF4749)

    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_000077.7 Reference GRCm39 C57BL/6J

      Range
      53945754..53959814 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030246067.1XP_030101927.1  PDZ and LIM domain protein 4 isoform X1

      Conserved Domains (2) summary
      cl02475
      Location:196248
      LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
      pfam15936
      Location:91171
      DUF4749; Domain of unknown function (DUF4749)