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

Gene ID: 9124, updated on 4-Dec-2022

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
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Genomic context

See PDLIM1 in Genome Data Viewer
Location:
10q23.33
Exon count:
7
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (95237572..95291003, complement)
110 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 Sharpr-MPRA regulatory region 8644 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr10:96990347-96990915 and GRCh37_chr10:96990916-96991485 Neighboring gene CRISPRi-validated cis-regulatory element chr10.3436 Neighboring gene Sharpr-MPRA regulatory region 12220 Neighboring gene sorbin and SH3 domain containing 1

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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables actin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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
PubMed 
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
PubMed 
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
PubMed 
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
PubMed 
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
PubMed 
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
PubMed 
located_in focal adhesion HDA PubMed 
is_active_in stress fiber IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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)

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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_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
    O00151, 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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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)