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Pdlim1 PDZ and LIM domain 1 (elfin) [ Mus musculus (house mouse) ]

Gene ID: 54132, updated on 12-May-2024

Summary

Official Symbol
Pdlim1provided by MGI
Official Full Name
PDZ and LIM domain 1 (elfin)provided by MGI
Primary source
MGI:MGI:1860611
See related
Ensembl:ENSMUSG00000055044 AllianceGenome:MGI:1860611
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
CLP36; Clim1; mClim1
Summary
Enables transcription coactivator activity. Acts upstream of or within regulation of transcription by RNA polymerase II. Part of transcription regulator complex. Is expressed in several structures, including alimentary system; branchial arch; genitourinary system; heart; and sensory organ. Orthologous to human PDLIM1 (PDZ and LIM domain 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in large intestine adult (RPKM 123.7), placenta adult (RPKM 92.4) and 19 other tissues See more
Orthologs
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Genomic context

See Pdlim1 in Genome Data Viewer
Location:
19 C3; 19 34.24 cM
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 19 NC_000085.7 (40210683..40260060, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (40222239..40271616, complement)

Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene nuclear receptor subfamily 1, group D, member 2 pseudogene Neighboring gene STARR-seq mESC enhancer starr_46128 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene Neighboring gene STARR-seq mESC enhancer starr_46129 Neighboring gene CapStarr-seq enhancer MGSCv37_chr19:40331968-40332256 Neighboring gene STARR-seq mESC enhancer starr_46132 Neighboring gene predicted gene, 41845 Neighboring gene predicted gene 5693

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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (5) 
  • Gene trapped (2) 

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables actin binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables actin 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 transcription coactivator activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in actin cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in actin cytoskeleton organization ISO
Inferred from Sequence Orthology
more info
 
involved_in establishment or maintenance of actin cytoskeleton polarity ISO
Inferred from Sequence Orthology
more info
 
involved_in fibroblast migration ISO
Inferred from Sequence Orthology
more info
 
involved_in heart development IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in maintenance of cell polarity ISO
Inferred from Sequence Orthology
more info
 
involved_in muscle structure development IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in 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 Z disc ISO
Inferred from Sequence Orthology
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
 
part_of filamentous actin IBA
Inferred from Biological aspect of Ancestor
more info
 
is_active_in stress fiber IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in stress fiber ISO
Inferred from Sequence Orthology
more info
 
part_of transcription regulator complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
PDZ and LIM domain protein 1
Names
C-terminal LIM domain protein 1
LIM domain protein CLP-36
carboxyl terminal LIM domain protein 1
elfin

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_016861.4NP_058557.2  PDZ and LIM domain protein 1

    See identical proteins and their annotated locations for NP_058557.2

    Status: VALIDATED

    Source sequence(s)
    AF053367, AK076285, AK158992
    Consensus CDS
    CCDS37977.1
    UniProtKB/Swiss-Prot
    O70400, Q99K93
    UniProtKB/TrEMBL
    Q3TZ17
    Related
    ENSMUSP00000064545.6, ENSMUST00000068439.13
    Conserved Domains (3) summary
    cd09448
    Location:258309
    LIM_CLP36; This family represents the LIM domain of CLP36
    cd00992
    Location:581
    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:136228
    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_000085.7 Reference GRCm39 C57BL/6J

    Range
    40210683..40260060 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)