pdlim5a PDZ and LIM domain 5a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: pdlim5aprovided by ZNC
Official Full Name: PDZ and LIM domain 5aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-040718-401
See related: Ensembl:ENSDARG00000101777 AllianceGenome:ZFIN:ZDB-GENE-040718-401
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: pdlim5; zgc:91978
Summary: Predicted to enable actin binding activity and muscle alpha-actinin binding activity. Predicted to be involved in actin cytoskeleton organization; heart development; and muscle structure development. Predicted to be part of filamentous actin. Predicted to be active in Z disc; adherens junction; and stress fiber. Is expressed in several structures, including cephalic musculature; digestive system; dorsal aorta; nervous system; and notochord. Orthologous to human PDLIM5 (PDZ and LIM domain 5). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 5

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	5	NC_007116.7 (7722001..7844283, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	5	NC_007116.6 (7217353..7339627, complement)

Chromosome 5 - NC_007116.7 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

findings show the temporal & spatial expression patterns of the 3 Enigma family members & their PDZ & LIM domain encoding splice forms during embryogenesis
Title: Characterization of the Enigma family in zebrafish.

Submit: New GeneRIF Correction

General gene information

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Markers

fd99d03.x1 (e-PCR)
- UniSTS:195867

G40706 (e-PCR)
- UniSTS:70720

fk09c07.x1 (e-PCR)
- UniSTS:200569

z8921 (e-PCR), detects polymorphism
- UniSTS:204976

G39683 (e-PCR)
- UniSTS:17394

Gene Ontology Provided by ZFIN

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

Process	Evidence Code	Pubs
involved_in actin cytoskeleton organization	IBA Inferred from Biological aspect of Ancestor 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

Component	Evidence Code	Pubs
is_active_in Z disc	IBA Inferred from Biological aspect of Ancestor more info
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor 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

General protein information

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Preferred Names: PDZ and LIM domain protein 5; PDZ and LIM domain protein 5a

Names: DKEYP-100D11.1; ENH; PDZ and LIM domain 5

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_001002654.2 → NP_001002654.2 PDZ and LIM domain protein 5a

Status: VALIDATED

Source sequence(s)

CT737133, FO905009, FP067398

UniProtKB/TrEMBL

A0A0R4IN44, A0A8M9Q332, Q6DG04

Related

ENSDARP00000135287.1, ENSDART00000162626.2

Conserved Domains (5) summary

cd09361
Location:375 → 426

LIM1_Enigma_like; The first LIM domain of Enigma-like family

cd09362
Location:434 → 485

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd00992
Location:7 → 83

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) ...

cl02475
Location:493 → 547

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

pfam15936
Location:185 → 281

DUF4749; Domain of unknown function (DUF4749)

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007116.7 Reference GRCz11 Primary Assembly

Range

7722001..7844283 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017356060.2 → XP_017211549.1 PDZ and LIM domain protein 5 isoform X1

UniProtKB/TrEMBL

A0A8M6Z6A6, Q6DG04
XM_017356059.2 → XP_017211548.1 PDZ and LIM domain protein 5 isoform X1

UniProtKB/TrEMBL

A0A8M6Z6A6, Q6DG04
XM_021476074.1 → XP_021331749.1 PDZ and LIM domain protein 5 isoform X2

Related

ENSDARP00000132622.1, ENSDART00000158374.2

Conserved Domains (5) summary

cd09361
Location:375 → 426

LIM1_Enigma_like; The first LIM domain of Enigma-like family

cd09362
Location:434 → 485

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd00992
Location:7 → 83

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) ...

cl02475
Location:493 → 547

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

pfam15936
Location:185 → 281

DUF4749; Domain of unknown function (DUF4749)
XM_021476079.1 → XP_021331754.1 PDZ and LIM domain protein 5 isoform X6

UniProtKB/TrEMBL

A0A8M9Q337

Conserved Domains (5) summary

cd09361
Location:263 → 314

LIM1_Enigma_like; The first LIM domain of Enigma-like family

cd09362
Location:322 → 373

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd00992
Location:7 → 83

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) ...

cl02475
Location:381 → 435

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

cl25776
Location:137 → 169

DUF4749; Domain of unknown function (DUF4749)
XM_021476076.1 → XP_021331751.1 PDZ and LIM domain protein 5 isoform X4

UniProtKB/TrEMBL

A0A8M9Q8D9, Q6DG04

Conserved Domains (5) summary

cd09361
Location:269 → 320

LIM1_Enigma_like; The first LIM domain of Enigma-like family

cd09362
Location:328 → 379

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd00992
Location:7 → 83

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) ...

cl02475
Location:387 → 441

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

cl25776
Location:143 → 175

DUF4749; Domain of unknown function (DUF4749)
XM_021476078.1 → XP_021331753.1 PDZ and LIM domain protein 5 isoform X5

UniProtKB/TrEMBL

A0A8M9PXB6

Conserved Domains (5) summary

cd09361
Location:264 → 315

LIM1_Enigma_like; The first LIM domain of Enigma-like family

cd09362
Location:323 → 374

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd00992
Location:7 → 83

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) ...

cl02475
Location:382 → 436

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

cl25776
Location:138 → 170

DUF4749; Domain of unknown function (DUF4749)
XM_021476075.1 → XP_021331750.1 PDZ and LIM domain protein 5 isoform X3

UniProtKB/TrEMBL

A0A8M9QDQ6, Q6DG04

Conserved Domains (5) summary

cd09361
Location:270 → 321

LIM1_Enigma_like; The first LIM domain of Enigma-like family

cd09362
Location:329 → 380

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd00992
Location:7 → 83

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) ...

cl02475
Location:388 → 442

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

cl25776
Location:144 → 176

DUF4749; Domain of unknown function (DUF4749)
XM_021476080.1 → XP_021331755.1 PDZ and LIM domain protein 5 isoform X7

UniProtKB/TrEMBL

A0A8M9QDR0

Related

ENSDARP00000135718.1, ENSDART00000157661.2

Conserved Domains (2) summary

cd00992
Location:7 → 83

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:185 → 287

DUF4749; Domain of unknown function (DUF4749)