Pdlim7 PDZ and LIM domain 7 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Pdlim7provided by MGI
Official Full Name: PDZ and LIM domain 7provided by MGI
Primary source: MGI:MGI:1914649
See related: Ensembl:ENSMUSG00000021493 AllianceGenome:MGI:1914649
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: LMP
Summary: Predicted to enable actin binding activity and muscle alpha-actinin binding activity. Acts upstream of or within actin cytoskeleton organization. Located in cytoplasm; ruffle; and stress fiber. Is expressed in several structures, including cardiovascular system; gut; limb primordium; respiratory system; and tooth. Orthologous to human PDLIM7 (PDZ and LIM domain 7). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in bladder adult (RPKM 74.8), ovary adult (RPKM 59.7) and 26 other tissues See more
Orthologs: human all
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Genomic context

Location:: 13 B1; 13 30.06 cM

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	13	NC_000079.7 (55645300..55661281, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	13	NC_000079.6 (55497487..55513473, complement)

Chromosome 13 - NC_000079.7 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?

PDLIM7 Synergizes With PDLIM2 and p62/Sqstm1 to Inhibit Inflammatory Signaling by Promoting Degradation of the p65 Subunit of NF-kappaB.
Title: PDLIM7 Synergizes With PDLIM2 and p62/Sqstm1 to Inhibit Inflammatory Signaling by Promoting Degradation of the p65 Subunit of NF-κB.
primary endogenous regulator of platelet-dependent hemostasis
Title: Pdlim7 Regulates Arf6-Dependent Actin Dynamics and Is Required for Platelet-Mediated Thrombosis in Mice.
PDLIM7 is a bona fide skeletal muscle substrate of Nedd4-1.
Title: PDLIM7 is a novel target of the ubiquitin ligase Nedd4-1 in skeletal muscle.
findings describe a positive regulatory effect of LMP-1 on BMP-2 expression and BMP-2-mediated osteogenesis. This effect occurs through activation of ERK1/2 pathway and subsequent upregulation of Runx2 transactivity.
Title: LIM Mineralization Protein-1 Enhances Bone Morphogenetic Protein-2-Mediated Osteogenesis Through Activation of ERK1/2 MAPK Pathway and Upregulation of Runx2 Transactivity.
LMP is an important determinant of weight and length, female bone density, and marrow stromal cell propensity for mineralization.
Title: Lim mineralization protein-1 knockout mice have reduced spine trabecular bone density on microcomputed tomography due to decreased bone morphogenetic protein responsiveness.
These findings reveal a novel and unexpected function for Pdlim7 in maintaining proper hemostasis in neonatal and adult mice.
Title: Loss of the cytoskeletal protein Pdlim7 predisposes mice to heart defects and hemostatic dysfunction.
LMP-1 showed spatiotemporal expression patterns during molar development.[LMP-1]
Title: Immunohistochemical localization of LIM mineralization protein 1 during mouse molar development.
the LIM domain protein Enigma directly interacts with MDM2 to form a ternary complex with p53 in embryonic fibroblasts
Title: Enigma negatively regulates p53 through MDM2 and promotes tumor cell survival in mice.

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Variation

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Alleles

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

Gene trapped (1)
Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MARC_8185-8186:996688374:1 (e-PCR)
- UniSTS:269919

AV007930 (e-PCR)
- UniSTS:164527

Gene Ontology Provided by MGI

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
acts_upstream_of_or_within actin cytoskeleton organization	IPI Inferred from Physical Interaction more info	PubMed
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in heart development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation more info
involved_in muscle structure development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within ossification	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of osteoblast differentiation	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 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 adherens junction	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
part_of filamentous actin	IBA Inferred from Biological aspect of Ancestor more info
located_in focal adhesion	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in ruffle	IDA Inferred from Direct Assay more info	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

General protein information

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Preferred Names: PDZ and LIM domain protein 7

Names: LIM mineralization protein; protein enigma

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_001114087.2 → NP_001107559.1 PDZ and LIM domain protein 7 isoform b

See identical proteins and their annotated locations for NP_001107559.1

Status: VALIDATED

Description

Transcript Variant: This variant (b) lacks several exons, and uses an alternate 3'-terminal exon, compared to variant a. This results in a novel 3' coding region and 3' UTR, compared to variant a. The encoded isoform (b) has a shorter and distinct C-terminus, compared to isoform a.

Source sequence(s)

AK077998, BY262003

Consensus CDS

CCDS49276.1

UniProtKB/TrEMBL

Q8BVJ7

Related

ENSMUSP00000070153.7, ENSMUST00000069968.13

Conserved Domains (2) summary

cd00992
Location:5 → 79

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) ...

cl02526
Location:34 → 133

Peptidase_S41; C-terminal processing peptidase family S41
NM_001114088.2 → NP_001107560.1 PDZ and LIM domain protein 7 isoform a

See identical proteins and their annotated locations for NP_001107560.1

Status: VALIDATED

Description

Transcript Variant: This variant (a) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AK167476, BY262003, CT009762

Consensus CDS

CCDS49275.1

UniProtKB/Swiss-Prot

Q3TJD7, Q80ZY6, Q810S3, Q8C1S4, Q9CRA1

Related

ENSMUSP00000047173.7, ENSMUST00000046246.13

Conserved Domains (4) summary

cd09452
Location:282 → 333

LIM1_Enigma; The first LIM domain of Enigma

cd09456
Location:341 → 392

LIM2_Enigma; The second LIM domain of Enigma

cd09458
Location:400 → 454

LIM3_Enigma; The third LIM domain of Enigma

cd00992
Location:5 → 79

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) ...
NM_026131.4 → NP_080407.3 PDZ and LIM domain protein 7 isoform c

See identical proteins and their annotated locations for NP_080407.3

Status: VALIDATED

Description

Transcript Variant: This variant (c) has multiple differences in the coding region, and uses an alternate 3'-terminal exon, compared to variant a. The encoded isoform (c) is shorter and has multiple distinct segments, compared to isoform a.

Source sequence(s)

AK003338, AK077998, BY262003

Consensus CDS

CCDS26547.1

UniProtKB/Swiss-Prot

Q3TJD7

UniProtKB/TrEMBL

Q8BVJ7

Related

ENSMUSP00000064219.7, ENSMUST00000069929.13

Conserved Domains (2) summary

cd00992
Location:5 → 79

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) ...

cl02526
Location:22 → 164

Peptidase_S41; C-terminal processing peptidase family S41

RNA

NR_104287.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (d) lacks several exons and contains two alternate exons, compared to variant a. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant a, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK003338, AK033091, AK077998, BY262003

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

NC_000079.7 Reference GRCm39 C57BL/6J

Range

55645300..55661281 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006517346.4 → XP_006517409.1 PDZ and LIM domain protein 7 isoform X2

See identical proteins and their annotated locations for XP_006517409.1

Related

ENSMUST00000128910.8

Conserved Domains (3) summary

cd09456
Location:193 → 244

LIM2_Enigma; The second LIM domain of Enigma

pfam15936
Location:8 → 37

DUF4749; Domain of unknown function (DUF4749)

cl02475
Location:252 → 306

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
XM_036158140.1 → XP_036014033.1 PDZ and LIM domain protein 7 isoform X2

Conserved Domains (3) summary

cd09456
Location:193 → 244

LIM2_Enigma; The second LIM domain of Enigma

pfam15936
Location:8 → 37

DUF4749; Domain of unknown function (DUF4749)

cl02475
Location:252 → 306

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
XM_006517345.4 → XP_006517408.1 PDZ and LIM domain protein 7 isoform X2

See identical proteins and their annotated locations for XP_006517408.1

Conserved Domains (3) summary

cd09456
Location:193 → 244

LIM2_Enigma; The second LIM domain of Enigma

pfam15936
Location:8 → 37

DUF4749; Domain of unknown function (DUF4749)

cl02475
Location:252 → 306

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
XM_011244558.3 → XP_011242860.1 PDZ and LIM domain protein 7 isoform X2

See identical proteins and their annotated locations for XP_011242860.1

Conserved Domains (3) summary

cd09456
Location:193 → 244

LIM2_Enigma; The second LIM domain of Enigma

pfam15936
Location:8 → 37

DUF4749; Domain of unknown function (DUF4749)

cl02475
Location:252 → 306

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
XM_006517344.4 → XP_006517407.1 PDZ and LIM domain protein 7 isoform X1

Conserved Domains (5) summary

cd09452
Location:248 → 299

LIM1_Enigma; The first LIM domain of Enigma

cd09456
Location:307 → 358

LIM2_Enigma; The second LIM domain of Enigma

cd09458
Location:366 → 420

LIM3_Enigma; The third LIM domain of Enigma

cd00992
Location:5 → 79

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:116 → 151

DUF4749; Domain of unknown function (DUF4749)
XM_006517349.2 → XP_006517412.1 PDZ and LIM domain protein 7 isoform X3

Conserved Domains (2) summary

PLN00049
Location:34 → 133

PLN00049; carboxyl-terminal processing protease; Provisional

cd00992
Location:5 → 79

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) ...