Pdlim7 PDZ and LIM domain 7 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Pdlim7provided by RGD
Official Full Name: PDZ and LIM domain 7provided by RGD
Primary source: RGD:628769
See related: Ensembl:ENSRNOG00000013653 AllianceGenome:RGD:628769
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Enigma
Summary: Predicted to enable actin binding activity and muscle alpha-actinin binding activity. Involved in positive regulation of osteoblast differentiation. Predicted to be located in several cellular components, including focal adhesion; nucleoplasm; and ruffle. Predicted to be part of filamentous actin. Predicted to be active in Z disc; adherens junction; and stress fiber. Orthologous to human PDLIM7 (PDZ and LIM domain 7). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Muscle (RPKM 461.2), Heart (RPKM 130.7) and 7 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 17p14

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	17	NC_086035.1 (9129603..9144956)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	17	NC_051352.1 (9124565..9139814)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	17	NC_005116.4 (9653510..9668715)

Chromosome 17 - NC_086035.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
These findings indicate that CLP36 plays a critical role in stress fiber formation and the assembly of focal adhesions in BeWo cells.
Title: The PDZ-LIM protein CLP36 is required for actin stress fiber formation and focal adhesion assembly in BeWo cells.
In rats, estrogen was found to up-regulate enigma(LIM domain protein) genes in smooth muscle vascular cells.
Title: Caveolin-1, Id3a and two LIM protein genes are upregulated by estrogen in vascular smooth muscle cells.

Submit: New GeneRIF Correction

General gene information

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Markers

RH137205 (e-PCR)
- UniSTS:219293

RH129693 (e-PCR)
- UniSTS:212989

Gene Ontology Provided by RGD

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 actin cytoskeleton organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within actin cytoskeleton organization	ISO Inferred from Sequence Orthology 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 positive regulation of osteoblast differentiation	IDA Inferred from Direct Assay 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	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	IEA Inferred from Electronic Annotation more info
located_in adherens junction	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
part_of filamentous actin	IBA Inferred from Biological aspect of Ancestor more info
located_in focal adhesion	IEA Inferred from Electronic Annotation more info
located_in focal adhesion	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in ruffle	IEA Inferred from Electronic Annotation more info
located_in ruffle	ISO Inferred from Sequence Orthology more info
is_active_in stress fiber	IBA Inferred from Biological aspect of Ancestor more info
located_in stress fiber	IEA Inferred from Electronic Annotation more info
located_in stress fiber	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: PDZ and LIM domain protein 7

Names: LIM mineralization protein 2; LMP; enigma (LIM domain 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_173125.2 → NP_775148.1 PDZ and LIM domain protein 7

See identical proteins and their annotated locations for NP_775148.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000017

UniProtKB/Swiss-Prot

Q9Z1Z9

UniProtKB/TrEMBL

A0A8I6AKU2, A6KAR4

Related

ENSRNOP00000018899.3, ENSRNOT00000018899.4

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) ...

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086035.1 Reference GRCr8

Range

9129603..9144956

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039095428.2 → XP_038951356.1 PDZ and LIM domain protein 7 isoform X1

UniProtKB/TrEMBL

A0A8I6AKU2

Conserved Domains (6) summary

cd09452
Location:289 → 340

LIM1_Enigma; The first LIM domain of Enigma

cd09456
Location:348 → 399

LIM2_Enigma; The second LIM domain of Enigma

cd09458
Location:407 → 461

LIM3_Enigma; The third LIM domain of Enigma

PHA03247
Location:11 → 261

PHA03247; large tegument protein UL36; 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) ...

pfam15936
Location:163 → 192

DUF4749; Domain of unknown function (DUF4749)
XM_006253610.5 → XP_006253672.3 PDZ and LIM domain protein 7 isoform X2

UniProtKB/TrEMBL

A0A8I6AKU2, A0A8I6GK07

Related

ENSRNOP00000092912.1
XM_063276122.1 → XP_063132192.1 PDZ and LIM domain protein 7 isoform X3
XM_039095429.2 → XP_038951357.1 PDZ and LIM domain protein 7 isoform X4

Conserved Domains (4) summary

cd09452
Location:289 → 340

LIM1_Enigma; The first LIM domain of Enigma

PHA03247
Location:82 → 259

PHA03247; large tegument protein UL36; 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) ...

pfam15936
Location:163 → 192

DUF4749; Domain of unknown function (DUF4749)
XM_039095430.2 → XP_038951358.1 PDZ and LIM domain protein 7 isoform X6

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) ...

pfam15936
Location:170 → 192

DUF4749; Domain of unknown function (DUF4749)
XM_006253611.5 → XP_006253673.3 PDZ and LIM domain protein 7 isoform X7

UniProtKB/TrEMBL

A0A8I6AH90, A6KAR6

Related

ENSRNOP00000092278.1

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) ...

pfam15936
Location:163 → 185

DUF4749; Domain of unknown function (DUF4749)
XM_006253612.5 → XP_006253674.3 PDZ and LIM domain protein 7 isoform X9

UniProtKB/TrEMBL

A6KAR7

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) ...

pfam15936
Location:129 → 151

DUF4749; Domain of unknown function (DUF4749)
XM_063276123.1 → XP_063132193.1 PDZ and LIM domain protein 7 isoform X1
XM_063276124.1 → XP_063132194.1 PDZ and LIM domain protein 7 isoform X5

UniProtKB/Swiss-Prot

Q9Z1Z9

UniProtKB/TrEMBL

A6KAR4
XM_039095433.2 → XP_038951361.1 PDZ and LIM domain protein 7 isoform X8

UniProtKB/TrEMBL

A6KAS0

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_039095432.2 → XP_038951360.1 PDZ and LIM domain protein 7 isoform X8

UniProtKB/TrEMBL

A6KAS0

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