Ldb1 LIM domain binding 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ldb1provided by RGD
Official Full Name: LIM domain binding 1provided by RGD
Primary source: RGD:1310359
See related: EnsemblRapid:ENSRNOG00000018468 AllianceGenome:RGD:1310359
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 several functions, including LIM domain binding activity; protein homodimerization activity; and transcription coactivator activity. Predicted to contribute to DNA binding activity. Predicted to be involved in several processes, including negative regulation of erythrocyte differentiation; positive regulation of hemoglobin biosynthetic process; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including cerebellar Purkinje cell differentiation; epithelial structure maintenance; and hair follicle development. Predicted to be located in cell leading edge and chromatin. Predicted to be part of beta-catenin-TCF complex. Predicted to be active in nucleus. Orthologous to human LDB1 (LIM domain binding 1). [provided by Alliance of Genome Resources, Oct 2024]
Expression: Biased expression in Thymus (RPKM 351.2), Spleen (RPKM 256.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q54

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (254813161..254838931, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (244864168..244890007, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (265772729..265798442, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
contributes_to DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables LIM domain binding	IBA Inferred from Biological aspect of Ancestor more info
enables LIM domain binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info
enables transcription coregulator activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within anterior/posterior axis specification	ISO Inferred from Sequence Orthology more info
acts_upstream_of cell adhesion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular component assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cerebellar Purkinje cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cerebellum development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within epithelial structure maintenance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within gastrulation with mouth forming second	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within hair follicle development	ISO Inferred from Sequence Orthology more info
involved_in head development	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 erythrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in nervous system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of hemoglobin biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription elongation by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell migration	ISO Inferred from Sequence Orthology more info
involved_in regulation of focal adhesion assembly	ISO Inferred from Sequence Orthology more info
involved_in regulation of kinase activity	IEA Inferred from Electronic Annotation more info
involved_in regulation of kinase activity	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within somatic stem cell population maintenance	ISO Inferred from Sequence Orthology more info
involved_in transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery	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
part_of beta-catenin-TCF complex	ISO Inferred from Sequence Orthology more info
located_in cell leading edge	ISO Inferred from Sequence Orthology more info
located_in chromatin	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	IBA Inferred from Biological aspect of Ancestor more info
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: LIM domain-binding protein 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.