Lmo4 LIM domain only 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Lmo4provided by RGD
Official Full Name: LIM domain only 4provided by RGD
Primary source: RGD:1305670
See related: Ensembl:ENSRNOG00000009205 AllianceGenome:RGD:1305670
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 metal ion binding activity. Predicted to be involved in positive regulation of kinase activity and regulation of cell migration. Predicted to act upstream of or within several processes, including cell differentiation in spinal cord; neural tube closure; and thymus development. Predicted to be located in cell leading edge and nucleus. Predicted to be part of RNA polymerase II transcription regulator complex. Orthologous to human LMO4 (LIM domain only 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Heart (RPKM 161.3), Thymus (RPKM 149.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 2q44

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (235924574..235941609, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (233264180..233280881, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (250218635..250235435, complement)

Chromosome 2 - NC_086020.1 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?

Authors provided the first evidence of in vivo nitration of Lmo4 in cisplatin ototoxicity.
Title: Downstream targets of Lmo4 are modulated by cisplatin in the inner ear of Wistar rats.
Data reveal that LMO4 is a rapidly induced downstream effector of ATP signaling that promotes neuron survival from hypoxia.
Title: Extracellular ATP-dependent upregulation of the transcription cofactor LMO4 promotes neuron survival from hypoxia.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables transcription corepressor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in motor neuron axon guidance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of protein-containing complex assembly	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein-containing complex assembly	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neural tube closure	ISO Inferred from Sequence Orthology more info
involved_in neural tube closure	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of cell activation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of cell fate specification	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell migration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within spinal cord association neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in spinal cord motor neuron cell fate specification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within spinal cord motor neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within thymus development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ventral spinal cord interneuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ventricular septum development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	ISO Inferred from Sequence Orthology more info
located_in cell leading edge	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: LIM domain transcription factor LMO4

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_001009708.1 → NP_001009708.1 LIM domain transcription factor LMO4

See identical proteins and their annotated locations for NP_001009708.1

Status: PROVISIONAL

Source sequence(s)

BC087700

UniProtKB/TrEMBL

F7EU01, Q5PPG8

Related

ENSRNOP00000062436.1, ENSRNOT00000067502.3

Conserved Domains (2) summary

cd09386
Location:23 → 77

LIM1_LMO4; The first LIM domain of LMO4 (LIM domain only protein 4)

cd09387
Location:87 → 141

LIM2_LMO4; The second LIM domain of LMO4 (LIM domain only protein 4)

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_086020.1 Reference GRCr8

Range

235924574..235941609 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006233438.4 → XP_006233500.1 LIM domain transcription factor LMO4 isoform X2

See identical proteins and their annotated locations for XP_006233500.1

UniProtKB/TrEMBL

F7EU01, Q5PPG8

Conserved Domains (2) summary

cd09386
Location:23 → 77

LIM1_LMO4; The first LIM domain of LMO4 (LIM domain only protein 4)

cd09387
Location:87 → 141

LIM2_LMO4; The second LIM domain of LMO4 (LIM domain only protein 4)
XM_063282227.1 → XP_063138297.1 LIM domain transcription factor LMO4 isoform X1
XM_063282228.1 → XP_063138298.1 LIM domain transcription factor LMO4 isoform X1