Ldb3 LIM domain binding 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ldb3provided by RGD
Official Full Name: LIM domain binding 3provided by RGD
Primary source: RGD:1564875
See related: EnsemblRapid:ENSRNOG00000059166 AllianceGenome:RGD:1564875
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: ZASP; RGD1564875
Summary: Enables enzyme binding activity. Predicted to be involved in actin cytoskeleton organization; heart development; and muscle structure development. Predicted to act upstream of or within sarcomere organization. Located in Z disc. Human ortholog(s) of this gene implicated in dilated cardiomyopathy; dilated cardiomyopathy 1C; distal myopathy; and myofibrillar myopathy 4. Orthologous to human LDB3 (LIM domain binding 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Muscle (RPKM 1210.6) and Heart (RPKM 842.6) See more
Orthologs: human mouse all
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Genomic context

Location:: 16p15

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	16	NC_086034.1 (9862161..9926338, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	16	NC_051351.1 (9855768..9920108, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	16	NC_005115.4 (10878348..10943016, complement)

Chromosome 16 - NC_086034.1 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?

Downregulation of Cypher induces apoptosis in cardiomyocytes via Akt/p38 MAPK signaling pathway.
Title: Downregulation of Cypher induces apoptosis in cardiomyocytes via Akt/p38 MAPK signaling pathway.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH133871 (e-PCR)
- UniSTS:217154

LDB3 (e-PCR)
- UniSTS:511832

stSG622338 (e-PCR)
- UniSTS:455347

RH133236 (e-PCR)
- UniSTS:216519

Ldb3 (e-PCR), detects polymorphism
- UniSTS:515316

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables actin binding	IBA Inferred from Biological aspect of Ancestor more info
enables cytoskeletal protein binding	ISO Inferred from Sequence Orthology more info
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
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 muscle alpha-actinin binding	ISO Inferred from Sequence Orthology more info
enables protein kinase C binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in actin cytoskeleton organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in biological_process	ND No biological Data available 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
acts_upstream_of_or_within sarcomere organization	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	IDA Inferred from Direct Assay more info	PubMed
located_in Z disc	ISO Inferred from Sequence Orthology more info
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor 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

General protein information

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Preferred Names: LIM domain-binding protein 3

Names: Cypher

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_001110490.2 → NP_001103960.1 LIM domain-binding protein 3 isoform 4

See identical proteins and their annotated locations for NP_001103960.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) differs in both UTR's and has multiple differences in the coding region, compared to variant 1. The encoded isoform (4) is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

FM122871, FN804937, JAXUCZ010000016

UniProtKB/TrEMBL

D4A1A2, Q5XIG1

Conserved Domains (2) summary

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:148 → 249

DUF4749; Domain of unknown function (DUF4749)
NM_001277158.1 → NP_001264087.1 LIM domain-binding protein 3 isoform 3

See identical proteins and their annotated locations for NP_001264087.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in both UTR's and has multiple differences in the coding region, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1. Both variants 3 and 4 encode the same isoform.

Source sequence(s)

FM122871, FN804937, JAXUCZ010000016

UniProtKB/TrEMBL

A0A0G2JXR0

Conserved Domains (2) summary

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:148 → 254

DUF4749; Domain of unknown function (DUF4749)
NM_001277159.1 → NP_001264088.1 LIM domain-binding protein 3 isoform 3

See identical proteins and their annotated locations for NP_001264088.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 3' UTR and has multiple differences in the coding region, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1. Both variants 3 and 4 encode the same isoform.

Source sequence(s)

FM122871, FN804937, JAXUCZ010000016

UniProtKB/TrEMBL

A0A0G2JXR0

Conserved Domains (2) summary

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:148 → 254

DUF4749; Domain of unknown function (DUF4749)
NM_001277165.1 → NP_001264094.1 LIM domain-binding protein 3 isoform 1

Status: VALIDATED

Description

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

Source sequence(s)

JAXUCZ010000016

UniProtKB/TrEMBL

A0A096MKD4

Related

ENSRNOP00000075243.3, ENSRNOT00000086627.3

Conserved Domains (6) summary

cd09362
Location:609 → 660

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd09454
Location:550 → 601

LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family

cd09460
Location:668 → 722

LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family

PHA03247
Location:381 → 531

PHA03247; large tegument protein UL36; Provisional

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:195 → 296

DUF4749; Domain of unknown function (DUF4749)
NM_001277166.1 → NP_001264095.1 LIM domain-binding protein 3 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks one internal exon and includes two alternate internal exons, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.

Source sequence(s)

JAXUCZ010000016

UniProtKB/TrEMBL

A0A096MKD4, A0A0G2K2C4

Related

ENSRNOP00000072185.1, ENSRNOT00000085414.3

Conserved Domains (6) summary

cd09362
Location:562 → 613

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd09454
Location:503 → 554

LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family

cd09460
Location:621 → 675

LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family

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) ...

pfam05687
Location:364 → 419

BES1_N; BES1/BZR1 plant transcription factor, N-terminal

pfam15936
Location:148 → 242

DUF4749; Domain of unknown function (DUF4749)

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_086034.1 Reference GRCr8

Range

9862161..9926338 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017600209.3 → XP_017455698.1 LIM domain-binding protein 3 isoform X3

UniProtKB/TrEMBL

A0A096MKD4

Conserved Domains (6) summary

cd09362
Location:609 → 660

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd09454
Location:550 → 601

LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family

cd09460
Location:668 → 722

LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family

PHA03247
Location:381 → 531

PHA03247; large tegument protein UL36; Provisional

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:195 → 296

DUF4749; Domain of unknown function (DUF4749)
XM_039094753.2 → XP_038950681.1 LIM domain-binding protein 3 isoform X3

UniProtKB/TrEMBL

A0A096MKD4

Conserved Domains (6) summary

cd09362
Location:609 → 660

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd09454
Location:550 → 601

LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family

cd09460
Location:668 → 722

LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family

PHA03247
Location:381 → 531

PHA03247; large tegument protein UL36; Provisional

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:195 → 296

DUF4749; Domain of unknown function (DUF4749)
XM_006252637.5 → XP_006252699.3 LIM domain-binding protein 3 isoform X1

UniProtKB/TrEMBL

A0A096MJ01, A0A096MKD4

Related

ENSRNOP00000070984.2, ENSRNOT00000087521.3

Conserved Domains (6) summary

cd09362
Location:654 → 705

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd09454
Location:595 → 646

LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family

cd09460
Location:713 → 767

LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family

PHA03247
Location:426 → 576

PHA03247; large tegument protein UL36; Provisional

cd00992
Location:50 → 126

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:240 → 341

DUF4749; Domain of unknown function (DUF4749)
XM_006252644.5 → XP_006252706.3 LIM domain-binding protein 3 isoform X8

UniProtKB/TrEMBL

A0A096MKD4

Conserved Domains (6) summary

cd09362
Location:545 → 596

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd09454
Location:486 → 537

LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family

cd09460
Location:604 → 658

LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family

PHA03247
Location:286 → 470

PHA03247; large tegument protein UL36; Provisional

cd00992
Location:50 → 126

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:193 → 294

DUF4749; Domain of unknown function (DUF4749)
XM_006252640.5 → XP_006252702.3 LIM domain-binding protein 3 isoform X4

UniProtKB/TrEMBL

A0A096MKD4

Conserved Domains (6) summary

cd09362
Location:607 → 658

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd09454
Location:548 → 599

LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family

cd09460
Location:666 → 720

LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family

PHA03247
Location:379 → 529

PHA03247; large tegument protein UL36; Provisional

cd00992
Location:50 → 126

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:193 → 294

DUF4749; Domain of unknown function (DUF4749)
XM_017600211.3 → XP_017455700.2 LIM domain-binding protein 3 isoform X7

UniProtKB/TrEMBL

A0A096MKD4

Conserved Domains (6) summary

cd09362
Location:550 → 601

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd09454
Location:491 → 542

LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family

cd09460
Location:609 → 663

LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family

PHA03247
Location:292 → 483

PHA03247; large tegument protein UL36; Provisional

cd00992
Location:50 → 126

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:193 → 299

DUF4749; Domain of unknown function (DUF4749)
XM_017600208.3 → XP_017455697.2 LIM domain-binding protein 3 isoform X2

UniProtKB/TrEMBL

A0A096MKD4, A0A0G2JYM0

Related

ENSRNOP00000070707.1, ENSRNOT00000083623.3

Conserved Domains (6) summary

cd09362
Location:612 → 663

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd09454
Location:553 → 604

LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family

cd09460
Location:671 → 725

LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family

PHA03247
Location:384 → 534

PHA03247; large tegument protein UL36; Provisional

cd00992
Location:50 → 126

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:193 → 299

DUF4749; Domain of unknown function (DUF4749)
XM_006252641.5 → XP_006252703.3 LIM domain-binding protein 3 isoform X5

UniProtKB/TrEMBL

A0A8I5Y5H4

Related

ENSRNOP00000076700.1, ENSRNOT00000104381.2

Conserved Domains (6) summary

cd09362
Location:592 → 643

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd09454
Location:533 → 584

LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family

cd09460
Location:651 → 705

LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family

PHA03247
Location:334 → 531

PHA03247; large tegument protein UL36; Provisional

cd00992
Location:50 → 126

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:240 → 341

DUF4749; Domain of unknown function (DUF4749)
XM_017600210.3 → XP_017455699.1 LIM domain-binding protein 3 isoform X6

UniProtKB/TrEMBL

A0A096MKD4
XM_006252645.5 → XP_006252707.3 LIM domain-binding protein 3 isoform X9

Conserved Domains (2) summary

cd00992
Location:50 → 126

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:240 → 341

DUF4749; Domain of unknown function (DUF4749)
XM_063275630.1 → XP_063131700.1 LIM domain-binding protein 3 isoform X10

UniProtKB/TrEMBL

A0A0G2JXR0

Related

ENSRNOP00000070370.2, ENSRNOT00000081631.3