U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    PDLIM7 PDZ and LIM domain 7 [ Homo sapiens (human) ]

    Gene ID: 9260, updated on 28-Oct-2024

    Summary

    Official Symbol
    PDLIM7provided by HGNC
    Official Full Name
    PDZ and LIM domain 7provided by HGNC
    Primary source
    HGNC:HGNC:22958
    See related
    Ensembl:ENSG00000196923 MIM:605903; AllianceGenome:HGNC:22958
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LMP1; LMP3
    Summary
    The protein encoded by this gene is representative of a family of proteins composed of conserved PDZ and LIM domains. LIM domains are proposed to function in protein-protein recognition in a variety of contexts including gene transcription and development and in cytoskeletal interaction. The LIM domains of this protein bind to protein kinases, whereas the PDZ domain binds to actin filaments. The gene product is involved in the assembly of an actin filament-associated complex essential for transmission of ret/ptc2 mitogenic signaling. The biological function is likely to be that of an adapter, with the PDZ domain localizing the LIM-binding proteins to actin filaments of both skeletal muscle and nonmuscle tissues. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in endometrium (RPKM 61.1), prostate (RPKM 52.9) and 22 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PDLIM7 in Genome Data Viewer
    Location:
    5q35.3
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (177483394..177497604, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (178026382..178040598, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (176910395..176924605, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene PRR7 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176874472-176875100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176876138-176876638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176876639-176877139 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16688 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176881361-176882061 Neighboring gene proline rich 7, synaptic Neighboring gene Sharpr-MPRA regulatory region 1974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16691 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16692 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176884168-176884868 Neighboring gene drebrin 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176894101-176894646 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:176895193-176895738 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:176895739-176896284 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176897377-176897922 Neighboring gene hESC enhancers GRCh37_chr5:176899493-176899996 and GRCh37_chr5:176899997-176900498 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176904724-176905224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176911017-176911732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176911733-176912448 Neighboring gene Sharpr-MPRA regulatory region 15492 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176918835-176919378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176919379-176919920 Neighboring gene Sharpr-MPRA regulatory region 583 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176923257-176923998 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176925479-176926218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23721 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176929555-176930508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176930509-176931460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23725 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23726 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23727 Neighboring gene docking protein 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:176943204-176944028 Neighboring gene DEAD-box helicase 41

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin binding IBA
    Inferred from Biological aspect of Ancestor
    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 
    Process Evidence Code Pubs
    involved_in actin cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    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 ossification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in receptor-mediated endocytosis TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in Z disc IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in actin cytoskeleton IDA
    Inferred from Direct Assay
    more info
     
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in adherens junction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    part_of filamentous actin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in focal adhesion IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in ruffle IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in stress fiber IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    PDZ and LIM domain protein 7
    Names
    1110003B01Rik
    LIM domain protein
    LMP
    Lim mineralization protein 3
    PDZ and LIM domain 7 (enigma)
    protein enigma

    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_005451.5NP_005442.2  PDZ and LIM domain protein 7 isoform 1

      See identical proteins and their annotated locations for NP_005442.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      BC001093, HY026171
      Consensus CDS
      CCDS4422.1
      UniProtKB/Swiss-Prot
      Q14250, Q5XG82, Q6NVZ5, Q96C91, Q9BXB8, Q9BXB9, Q9NR12
      Related
      ENSP00000348099.2, ENST00000355841.7
      Conserved Domains (5) summary
      cd09452
      Location:282333
      LIM1_Enigma; The first LIM domain of Enigma
      cd09456
      Location:341392
      LIM2_Enigma; The second LIM domain of Enigma
      cd09458
      Location:400454
      LIM3_Enigma; The third LIM domain of Enigma
      cd00992
      Location:579
      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) ...
      cl26464
      Location:81254
      Atrophin-1; Atrophin-1 family
    2. NM_203352.3NP_976227.1  PDZ and LIM domain protein 7 isoform 2

      See identical proteins and their annotated locations for NP_976227.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 2 which is shorter than isoform 1.
      Source sequence(s)
      AF345905, BC001093, HY026171
      Consensus CDS
      CCDS4423.1
      UniProtKB/Swiss-Prot
      Q9NR12
      Related
      ENSP00000352964.2, ENST00000359895.6
      Conserved Domains (5) summary
      cd09452
      Location:248299
      LIM1_Enigma; The first LIM domain of Enigma
      cd09456
      Location:307358
      LIM2_Enigma; The second LIM domain of Enigma
      cd09458
      Location:366420
      LIM3_Enigma; The third LIM domain of Enigma
      cd00992
      Location:579
      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:93147
      DUF4749; Domain of unknown function (DUF4749)
    3. NM_213636.3NP_998801.1  PDZ and LIM domain protein 7 isoform 4

      See identical proteins and their annotated locations for NP_998801.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks several exons and has an alternate 3' terminal exon, compared to variant 1. The resulting isoform (4) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      BC014521, HY026171
      Consensus CDS
      CCDS4424.1
      UniProtKB/TrEMBL
      H7BYK4
      Related
      ENSP00000347776.2, ENST00000355572.6
      Conserved Domains (1) summary
      cd00992
      Location:579
      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) ...

    RNA

    1. NR_103804.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) has an alternate splice site in the central region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC001093, BC067806, BU956109, HY026171
      Related
      ENST00000486828.6

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      177483394..177497604 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      178026382..178040598 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_203353.1: Suppressed sequence

      Description
      NM_203353.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.