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

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: human all
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Genomic context

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_000085.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Direct Knockdown of PDZ and LIM Domain 1 Using an Adenoviral Delivery System Accelerates Osteogenesis and Fracture Healing in Mice.
Title: Direct Knockdown of PDZ and LIM Domain 1 Using an Adenoviral Delivery System Accelerates Osteogenesis and Fracture Healing in Mice.
PDLIM1 inhibits cell migration and invasion in diabetic retinopathy via negatively regulating Wnt3a.
Title: PDLIM1 inhibits cell migration and invasion in diabetic retinopathy via negatively regulating Wnt3a.
autophagy regulates cytoskeleton organization mainly via degradation of PDLIM1 to facilitate the differentiation of spermatids
Title: Autophagy regulates spermatid differentiation via degradation of PDLIM1.
Data show an inhibitory function of CLP-36 in GPVI immunoreceptor tyrosine-based activation motif signaling and as a key regulator of arterial thrombosis.
Title: CLP36 is a negative regulator of glycoprotein VI signaling in platelets.
The LIM-homeodomain-related genes Lmo4 and Clim1 are initially expressed by both CPN and subcerebral PN in layer V, and only during mid to late differentiation does expression of Lmo4 and Clim1 become largely segregated into distinct neuronal subtypes.
Title: Lmo4 and Clim1 progressively delineate cortical projection neuron subtypes during development.
Clim1 protein plays an important role in the homeostasis of corneal epithelium and hair follicles.
Title: Co-factors of LIM domains (Clims/Ldb/Nli) regulate corneal homeostasis and maintenance of hair follicle stem cells.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (2)
Endonuclease-mediated (5)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH126574 (e-PCR)
- UniSTS:209697

Pdlim1 (e-PCR), detects polymorphism
- UniSTS:507378

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

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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)

NM_016861.4 → NP_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:258 → 309

LIM_CLP36; This family represents the LIM domain of CLP36

cd00992
Location:5 → 81

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:136 → 228

DUF4749; Domain of unknown function (DUF4749)