Limd1 LIM domain containing 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Limd1provided by RGD
Official Full Name: LIM domain containing 1provided by RGD
Primary source: RGD:1309830
See related: EnsemblRapid:ENSRNOG00000004837 AllianceGenome:RGD:1309830
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
Summary: Predicted to enable transcription corepressor activity. Predicted to be involved in several processes, including negative regulation of macromolecule biosynthetic process; negative regulation of osteoblast differentiation; and negative regulation of signal transduction. Predicted to act upstream of or within P-body assembly and miRNA-mediated post-transcriptional gene silencing. Predicted to be located in several cellular components, including focal adhesion; nucleoplasm; and plasma membrane. Predicted to be part of RISC complex and transcription regulator complex. Predicted to be active in P-body; adherens junction; and nucleus. Orthologous to human LIMD1 (LIM domain containing 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Heart (RPKM 246.9), Lung (RPKM 236.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 8q32

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (131998262..132045924)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (123121363..123168476)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (132553218..132598826)

Chromosome 8 - NC_086026.1 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?

SKI activates the Hippo pathway via LIMD1 to inhibit cardiac fibroblast activation.
Title: SKI activates the Hippo pathway via LIMD1 to inhibit cardiac fibroblast activation.

Submit: New GeneRIF Correction

General gene information

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Markers

RH139102 (e-PCR)
- UniSTS:221188

AU028871 (e-PCR)
- UniSTS:111910

D8Sunn1376 (e-PCR)
- UniSTS:518575

RH141178 (e-PCR)
- UniSTS:223174

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables transcription corepressor activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription corepressor activity	ISO Inferred from Sequence Orthology more info
enables transcription corepressor activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within P-body assembly	ISO Inferred from Sequence Orthology more info
involved_in cell migration	ISO Inferred from Sequence Orthology more info
involved_in cytoskeleton organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in cytoskeleton organization	ISO Inferred from Sequence Orthology more info
involved_in miRNA-mediated gene silencing by inhibition of translation	ISO Inferred from Sequence Orthology more info
involved_in miRNA-mediated gene silencing by inhibition of translation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within miRNA-mediated post-transcriptional gene silencing	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of canonical Wnt signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of hippo signaling	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of hippo signaling	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of hippo signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of osteoblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of osteoblast differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in osteoblast development	ISO Inferred from Sequence Orthology more info
involved_in osteoblast development	ISS Inferred from Sequence or Structural Similarity more info
involved_in phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of cell shape	ISO Inferred from Sequence Orthology more info
involved_in regulatory ncRNA-mediated gene silencing	IEA Inferred from Electronic Annotation more info
involved_in response to hypoxia	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to hypoxia	ISO Inferred from Sequence Orthology more info
involved_in response to hypoxia	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in P-body	IBA Inferred from Biological aspect of Ancestor more info
located_in P-body	ISO Inferred from Sequence Orthology more info
part_of RISC complex	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	ISO Inferred from Sequence Orthology more info
located_in adherens junction	ISS Inferred from Sequence or Structural Similarity more info
located_in anchoring junction	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in focal adhesion	ISO Inferred from Sequence Orthology more info
located_in focal adhesion	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: LIM domain-containing protein 1

Names: LIM domains containing 1

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_001112737.3 → NP_001106208.1 LIM domain-containing protein 1

See identical proteins and their annotated locations for NP_001106208.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000008

UniProtKB/Swiss-Prot

B5DEH0

UniProtKB/TrEMBL

A0A8I6A6E6

Conserved Domains (3) summary

cd09352
Location:459 → 512

LIM1_Ajuba_like; The first LIM domain of Ajuba-like proteins

cd09355
Location:524 → 576

LIM2_Ajuba_like; The second LIM domain of Ajuba-like proteins

cd09438
Location:584 → 645

LIM3_Ajuba_like; The third LIM domain of Ajuba-like proteins

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_086026.1 Reference GRCr8

Range

131998262..132045924

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039081663.2 → XP_038937591.1 LIM domain-containing protein 1 isoform X1

UniProtKB/Swiss-Prot

B5DEH0

UniProtKB/TrEMBL

A0A8I6A6E6

Related

ENSRNOP00000006554.5, ENSRNOT00000006554.9

Conserved Domains (3) summary

cd09352
Location:459 → 512

LIM1_Ajuba_like; The first LIM domain of Ajuba-like proteins

cd09355
Location:524 → 576

LIM2_Ajuba_like; The second LIM domain of Ajuba-like proteins

cd09438
Location:584 → 645

LIM3_Ajuba_like; The third LIM domain of Ajuba-like proteins
XM_063265665.1 → XP_063121735.1 LIM domain-containing protein 1 isoform X2