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

Gene ID: 498587, updated on 21-Jul-2018

Summary

Official Symbol
Ldb3provided by RGD
Official Full Name
LIM domain binding 3provided by RGD
Primary source
RGD:1564875
See related
Ensembl:ENSRNOG00000059166 Vega:OTTRNOG00000001792
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
Expression
Biased expression in Muscle (RPKM 1210.6) and Heart (RPKM 842.6) See more
Orthologs

Genomic context

See Ldb3 in Genome Data Viewer
Location:
16p15
Exon count:
19
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 16 NC_005115.4 (10878348..10943016, complement)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 16 NC_005115.3 (9203392..9267999, complement)

Chromosome 16 - NC_005115.4Genomic Context describing neighboring genes Neighboring gene multimerin 2 Neighboring gene uncharacterized LOC108353075 Neighboring gene bone morphogenetic protein receptor type 1A Neighboring gene NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 4-like Neighboring gene opsin 4 Neighboring gene WAPL cohesin release factor

Genomic regions, transcripts, and products

Expression

  • 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

General gene information

Markers

Gene Ontology Provided by RGD

Function Evidence Code Pubs
cytoskeletal protein binding ISO
Inferred from Sequence Orthology
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
molecular_function ND
No biological Data available
more info
 
muscle alpha-actinin binding IEA
Inferred from Electronic Annotation
more info
 
muscle alpha-actinin binding ISO
Inferred from Sequence Orthology
more info
 
protein kinase C binding IEA
Inferred from Electronic Annotation
more info
 
protein kinase C binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
biological_process ND
No biological Data available
more info
 
sarcomere organization IEA
Inferred from Electronic Annotation
more info
 
sarcomere organization ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
Z disc IDA
Inferred from Direct Assay
more info
PubMed 
Z disc ISO
Inferred from Sequence Orthology
more info
 
cytoskeleton IEA
Inferred from Electronic Annotation
more info
 
cytoskeleton ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
LIM domain-binding protein 3
Names
Cypher

NCBI Reference Sequences (RefSeq)

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)

  1. NM_001110490.2NP_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)
    AABR07024658, FM122871, FN804937
    UniProtKB/TrEMBL
    Q5XIG1
    Conserved Domains (2) summary
    cd00992
    Location:581
    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:148239
    DUF4749; Domain of unknown function (DUF4749)
  2. NM_001277158.1NP_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)
    AABR07024658, FM122871, FN804937
    UniProtKB/TrEMBL
    A0A0G2JXR0
    Related
    ENSRNOP00000070370.1, ENSRNOT00000081631.1
    Conserved Domains (2) summary
    cd00992
    Location:581
    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:148244
    DUF4749; Domain of unknown function (DUF4749)
  3. NM_001277159.1NP_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)
    AABR07024658, FM122871, FN804937
    UniProtKB/TrEMBL
    A0A0G2JXR0
    Conserved Domains (2) summary
    cd00992
    Location:581
    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:148244
    DUF4749; Domain of unknown function (DUF4749)
  4. NM_001277165.1NP_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)
    AABR07024658, AABR07072495
    UniProtKB/TrEMBL
    A0A096MJ01
    Related
    ENSRNOP00000070984.1, OTTRNOP00000001706, ENSRNOT00000087521.1, OTTRNOT00000002892
    Conserved Domains (6) summary
    cd09362
    Location:609660
    LIM2_Enigma_like; The second LIM domain of Enigma-like family
    cd09454
    Location:550601
    LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family
    cd09460
    Location:668722
    LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family
    cd00992
    Location:581
    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:411466
    BES1_N; BES1/BZR1 plant transcription factor, N-terminal
    pfam15936
    Location:195289
    DUF4749; Domain of unknown function (DUF4749)
  5. NM_001277166.1NP_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)
    AABR07024658, AABR07072495
    UniProtKB/TrEMBL
    A0A096MKD4
    Related
    ENSRNOP00000072185.1, ENSRNOT00000085414.1
    Conserved Domains (6) summary
    cd09362
    Location:562613
    LIM2_Enigma_like; The second LIM domain of Enigma-like family
    cd09454
    Location:503554
    LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family
    cd09460
    Location:621675
    LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family
    cd00992
    Location:581
    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:364419
    BES1_N; BES1/BZR1 plant transcription factor, N-terminal
    pfam15936
    Location:148242
    DUF4749; Domain of unknown function (DUF4749)

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

Reference Rnor_6.0 Primary Assembly

Genomic

  1. NC_005115.4 Reference Rnor_6.0 Primary Assembly

    Range
    10878348..10943016 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017600209.1XP_017455698.1  LIM domain-binding protein 3 isoform X1

    UniProtKB/TrEMBL
    A0A096MJ01
    Conserved Domains (6) summary
    cd09362
    Location:609660
    LIM2_Enigma_like; The second LIM domain of Enigma-like family
    cd09454
    Location:550601
    LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family
    cd09460
    Location:668722
    LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family
    cd00992
    Location:581
    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:411466
    BES1_N; BES1/BZR1 plant transcription factor, N-terminal
    pfam15936
    Location:195289
    DUF4749; Domain of unknown function (DUF4749)
  2. XM_006252644.3XP_006252706.2  LIM domain-binding protein 3 isoform X6

  3. XM_006252640.3XP_006252702.2  LIM domain-binding protein 3 isoform X3

    UniProtKB/TrEMBL
    A0A096MKD4
    Related
    ENSRNOP00000075243.1, OTTRNOP00000001705, ENSRNOT00000086627.1, OTTRNOT00000002891
    Conserved Domains (6) summary
    cd09362
    Location:562613
    LIM2_Enigma_like; The second LIM domain of Enigma-like family
    cd09454
    Location:503554
    LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family
    cd09460
    Location:621675
    LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family
    cd00992
    Location:581
    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:364419
    BES1_N; BES1/BZR1 plant transcription factor, N-terminal
    pfam15936
    Location:148242
    DUF4749; Domain of unknown function (DUF4749)
  4. XM_017600211.1XP_017455700.1  LIM domain-binding protein 3 isoform X5

  5. XM_017600208.1XP_017455697.1  LIM domain-binding protein 3 isoform X2

    Related
    ENSRNOP00000070707.1, ENSRNOT00000083623.1
  6. XM_006252641.3XP_006252703.2  LIM domain-binding protein 3 isoform X4

  7. XM_006252637.3XP_006252699.2  LIM domain-binding protein 3 isoform X1

    UniProtKB/TrEMBL
    A0A096MJ01
    Conserved Domains (6) summary
    cd09362
    Location:609660
    LIM2_Enigma_like; The second LIM domain of Enigma-like family
    cd09454
    Location:550601
    LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family
    cd09460
    Location:668722
    LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family
    cd00992
    Location:581
    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:411466
    BES1_N; BES1/BZR1 plant transcription factor, N-terminal
    pfam15936
    Location:195289
    DUF4749; Domain of unknown function (DUF4749)
  8. XM_017600210.1XP_017455699.1  LIM domain-binding protein 3 isoform X2

  9. XM_006252645.3XP_006252707.2  LIM domain-binding protein 3 isoform X7

Alternate Rn_Celera

Genomic

  1. AC_000084.1 Alternate Rn_Celera

    Range
    5298641..5360715
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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