PDLIM7 PDZ and LIM domain 7 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PDLIM7provided by HGNC
Official Full Name: PDZ and LIM domain 7provided by HGNC
Primary source: HGNC:HGNC:22958
See related: Ensembl:ENSG00000196923 MIM:605903; AllianceGenome:HGNC:22958
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: LMP1; LMP3
Summary: The protein encoded by this gene is representative of a family of proteins composed of conserved PDZ and LIM domains. LIM domains are proposed to function in protein-protein recognition in a variety of contexts including gene transcription and development and in cytoskeletal interaction. The LIM domains of this protein bind to protein kinases, whereas the PDZ domain binds to actin filaments. The gene product is involved in the assembly of an actin filament-associated complex essential for transmission of ret/ptc2 mitogenic signaling. The biological function is likely to be that of an adapter, with the PDZ domain localizing the LIM-binding proteins to actin filaments of both skeletal muscle and nonmuscle tissues. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]
Expression: Broad expression in endometrium (RPKM 61.1), prostate (RPKM 52.9) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q35.3

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (177483394..177497604, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (178026382..178040598, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (176910395..176924605, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Regulatory and Interacting Partners of PDLIM7 in Thyroid Cancer.
Title: Regulatory and Interacting Partners of PDLIM7 in Thyroid Cancer.
Epstein-Barr virus in gastric cancer and association with 30 bp del-latent membrane protein 1 polymorphism.
Title: Epstein-Barr virus in gastric cancer and association with 30 bp del-latent membrane protein 1 polymorphism.
Enigma of the cholesterol paradox in acute myocardial infarction: lessons from an 8-year follow-up of all-cause mortality in an age-matched and sex-matched case-control study with controls from the patients' recruitment area.
Title: Enigma of the cholesterol paradox in acute myocardial infarction: lessons from an 8-year follow-up of all-cause mortality in an age-matched and sex-matched case-control study with controls from the patients' recruitment area.
Overexpression of LMP-1 Decreases Apoptosis in Human Nucleus Pulposus Cells via Suppressing the NF-kappaB Signaling Pathway.
Title: Overexpression of LMP-1 Decreases Apoptosis in Human Nucleus Pulposus Cells via Suppressing the NF-κB Signaling Pathway.
Forces acting on integrins recruit Enigma family proteins (PDLIM5 AND PDLIM7) to trigger YAP activation during mechanotransduction.
Title: Enigma proteins regulate YAP mechanotransduction.
reported for the first time the effect of combining Yamanaka factors with hLMP-3 to induce osteoblast cells from MEF both in vitro and in vivo.
Title: Direct conversion of mouse embryonic fibroblast to osteoblast cells using hLMP-3 with Yamanaka factors.
A role for PDLIM7 and CDH18, regulating MDM2 protein in CDK4/6 inhibitor-treated cells.
Title: PDLIM7 and CDH18 regulate the turnover of MDM2 during CDK4/6 inhibitor therapy-induced senescence.
Cox proportional-hazards regression indicated that high LMP1 expression and the nasal floor thickness >2.0 mm or nasal septum thickness >2.5 mm were the independent risk factors for poor OS of ENKTL-NT (HR=3.0655, p=0.028; HR=2.3650, p=0.0452, respectively).
Title: Specific Soft-Tissue Invasion and LMP1 Expression Are Potential Indicators of Extranodal NK/T Cell Lymphoma, Nasal Type.
In enigma siRNA-transfected cells, cell viability, and the protein levels of AKT and survivin decreased.
Title: Enigma Plays Roles in Survival of Thyroid Carcinoma Cells through PI3K/AKT Signaling and Survivin.
LMOD1, SYNPO2, PDLIM7, PLN, and SYNM down-regulation reflect the altered phenotype of smooth muscle cells in vascular disease and could be early sensitive markers of SMC dedifferentiation.
Title: Phenotypic Modulation of Smooth Muscle Cells in Atherosclerosis Is Associated With Downregulation of LMOD1, SYNPO2, PDLIM7, PLN, and SYNM.

Submit: New GeneRIF Correction See all GeneRIFs (36)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH65364 (e-PCR)
- UniSTS:26687

SHGC-148959 (e-PCR)
- UniSTS:176705

RH80795 (e-PCR)
- UniSTS:92059

PDLIM7_8917 (e-PCR)
- UniSTS:471708

AV007930 (e-PCR)
- UniSTS:164527

STS_03 (e-PCR)
- UniSTS:257014

Gene Ontology Provided by GOA

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
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in heart development	IBA Inferred from Biological aspect of Ancestor more info
involved_in muscle structure development	IBA Inferred from Biological aspect of Ancestor more info
involved_in ossification	IEA Inferred from Electronic Annotation more info
involved_in receptor-mediated endocytosis	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
is_active_in Z disc	IBA Inferred from Biological aspect of Ancestor more info
located_in actin cytoskeleton	IDA Inferred from Direct Assay more info
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
located_in adherens junction	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
part_of filamentous actin	IBA Inferred from Biological aspect of Ancestor more info
located_in focal adhesion	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in ruffle	IEA Inferred from Electronic Annotation more info
is_active_in stress fiber	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: PDZ and LIM domain protein 7

Names: 1110003B01Rik; LIM domain protein; LMP; Lim mineralization protein 3; PDZ and LIM domain 7 (enigma); 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_005451.5 → NP_005442.2 PDZ and LIM domain protein 7 isoform 1

See identical proteins and their annotated locations for NP_005442.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

BC001093, HY026171

Consensus CDS

CCDS4422.1

UniProtKB/Swiss-Prot

Q14250, Q5XG82, Q6NVZ5, Q96C91, Q9BXB8, Q9BXB9, Q9NR12

Related

ENSP00000348099.2, ENST00000355841.7

Conserved Domains (5) 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) ...

cl26464
Location:81 → 254

Atrophin-1; Atrophin-1 family
NM_203352.3 → NP_976227.1 PDZ and LIM domain protein 7 isoform 2

See identical proteins and their annotated locations for NP_976227.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 2 which is shorter than isoform 1.

Source sequence(s)

AF345905, BC001093, HY026171

Consensus CDS

CCDS4423.1

UniProtKB/Swiss-Prot

Q9NR12

Related

ENSP00000352964.2, ENST00000359895.6

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:93 → 147

DUF4749; Domain of unknown function (DUF4749)
NM_213636.3 → NP_998801.1 PDZ and LIM domain protein 7 isoform 4

See identical proteins and their annotated locations for NP_998801.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks several exons and has an alternate 3' terminal exon, compared to variant 1. The resulting isoform (4) is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

BC014521, HY026171

Consensus CDS

CCDS4424.1

UniProtKB/TrEMBL

H7BYK4

Related

ENSP00000347776.2, ENST00000355572.6

Conserved Domains (1) 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) ...

RNA

NR_103804.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) has an alternate splice site in the central region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

BC001093, BC067806, BU956109, HY026171

Related

ENST00000486828.6

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

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

177483394..177497604 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060929.1 Alternate T2T-CHM13v2.0

Range

178026382..178040598 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_203353.1: Suppressed sequence

Description

NM_203353.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.