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    PDLIM1 PDZ and LIM domain 1 [ Homo sapiens (human) ]

    Gene ID: 9124, updated on 7-Jul-2024

    Summary

    Official Symbol
    PDLIM1provided by HGNC
    Official Full Name
    PDZ and LIM domain 1provided by HGNC
    Primary source
    HGNC:HGNC:2067
    See related
    Ensembl:ENSG00000107438 MIM:605900; AllianceGenome:HGNC:2067
    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
    CLIM1; CLP36; CLP-36; hCLIM1; HEL-S-112
    Summary
    This gene encodes a member of the enigma protein family. The protein contains two protein interacting domains, a PDZ domain at the amino terminal end and one to three LIM domains at the carboxyl terminal. It is a cytoplasmic protein associated with the cytoskeleton. The protein may function as an adapter to bring other LIM-interacting proteins to the cytoskeleton. Pseudogenes associated with this gene are located on chromosomes 3, 14 and 17. [provided by RefSeq, Oct 2012]
    Expression
    Ubiquitous expression in small intestine (RPKM 111.6), colon (RPKM 111.5) and 24 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See PDLIM1 in Genome Data Viewer
    Location:
    10q23.33
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (95237572..95291003, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (96116721..96170181, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (96997329..97050760, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2638 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2639 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:96961907-96962201 Neighboring gene pro-apoptotic WT1 regulator pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:96987152-96987893 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:96988638-96989207 Neighboring gene Sharpr-MPRA regulatory region 8644 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr10:96990347-96990915 and GRCh37_chr10:96990916-96991485 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:97000971-97001634 Neighboring gene acyl-CoA synthetase medium chain family member 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:97001635-97002298 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3792 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3793 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:97020155-97020844 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:97024067-97024842 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2641 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2642 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2643 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3795 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:97054719-97055315 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3797 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3798 Neighboring gene CRISPRi-validated cis-regulatory element chr10.3436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3799 Neighboring gene Sharpr-MPRA regulatory region 12220 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:97106670-97107322 Neighboring gene sorbin and SH3 domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2645 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3800 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:97190228-97190728 Neighboring gene Sharpr-MPRA regulatory region 10569 Neighboring gene VISTA enhancer hs2353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:97291131-97291878 Neighboring gene NANOG hESC enhancer GRCh37_chr10:97299485-97299986 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:97311480-97312414 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:97320711-97321473 Neighboring gene Sharpr-MPRA regulatory region 13709 Neighboring gene RPS3A pseudogene 36

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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?

    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 actin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables cadherin binding involved in cell-cell adhesion HDA PubMed 
    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 transcription coactivator activity IEA
    Inferred from Electronic Annotation
    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell-cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in establishment or maintenance of actin cytoskeleton polarity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in fibroblast migration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in heart development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in maintenance of cell polarity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in muscle structure development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to hypoxia IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to oxidative stress TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in stress fiber assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    is_active_in Z disc IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in Z disc IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in adherens junction HDA PubMed 
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoskeleton IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of filamentous actin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in focal adhesion HDA PubMed 
    is_active_in stress fiber IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in stress fiber IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transcription regulator complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    PDZ and LIM domain protein 1
    Names
    LIM domain protein CLP-36
    carboxyl terminal LIM domain protein 1
    elfin
    epididymis secretory protein Li 112

    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_020992.4NP_066272.1  PDZ and LIM domain protein 1

      See identical proteins and their annotated locations for NP_066272.1

      Status: REVIEWED

      Source sequence(s)
      AL160288, BC000915
      Consensus CDS
      CCDS7441.1
      UniProtKB/Swiss-Prot
      B2RBS6, O00151, Q5VZH5, Q9BPZ9
      UniProtKB/TrEMBL
      V9HW92
      Related
      ENSP00000360305.3, ENST00000329399.7
      Conserved Domains (3) summary
      cd09448
      Location:260311
      LIM_CLP36; This family represents the LIM domain of CLP36
      cd00992
      Location:1082
      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:138230
      DUF4749; Domain of unknown function (DUF4749)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      95237572..95291003 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      96116721..96170181 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)