lmx1bb LIM homeobox transcription factor 1, beta b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: lmx1bbprovided by ZNC
Official Full Name: LIM homeobox transcription factor 1, beta bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-050114-2
See related: Ensembl:ENSDARG00000068365 AllianceGenome:ZFIN:ZDB-GENE-050114-2
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: lmx1b; lmx1b.1
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Acts upstream of or within animal organ development and glutamatergic neuron differentiation. Predicted to be active in nucleus. Is expressed in several structures, including axis; midbrain hindbrain boundary neural keel; midbrain hindbrain boundary neural rod; nervous system; and otic vesicle. Human ortholog(s) of this gene implicated in focal segmental glomerulosclerosis and nail-patella syndrome. Orthologous to human LMX1B (LIM homeobox transcription factor 1 beta). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 8

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	8	NC_007119.7 (33260675..33381913, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	8	NC_007119.6 (33250999..33392767, complement)

Chromosome 8 - NC_007119.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

It has been proposed that the lmx1b-dependent pressure relief valve is required to maintain fluid homeostasis in the inner ear and other fluid-filled cavities.
Title: Lamellar projections in the endolymphatic sac act as a relief valve to regulate inner ear pressure.
Lmx1ba and Lmx1bb function at least partially redundantly in the spinal cord and three functional lmx1b alleles are required in zebrafish for correct numbers of excitatory spinal interneurons at later developmental stages.
Title: Lmx1b is required for the glutamatergic fates of a subset of spinal cord neurons.
Lmx1b and FoxC have roles in regulating podocin expression in podocytes
Title: Lmx1b and FoxC combinatorially regulate podocin expression in podocytes.
Results suggest that zebrafish lmx1b.1 and lmx1b.2 promote the survival of periocular mesenchymal cells that influence multiple signaling events required for proper ocular development.
Title: Lmx1b is essential for survival of periocular mesenchymal cells and influences Fgf-mediated retinal patterning in zebrafish.
lmx1b paralogues may contribute to the generation of diencephalic dopaminergic precursors
Title: Expression and function of nr4a2, lmx1b, and pitx3 in zebrafish dopaminergic and noradrenergic neuronal development.
Imx1b.1 regulation of wnt proteins, pax8 and fibroblast growth factor 8 (fgf8) maintains cell survival in the isthmocerebellar region
Title: Zebrafish Lmx1b.1 and Lmx1b.2 are required for maintenance of the isthmic organizer.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

fi59h04.y1 (e-PCR)
- UniSTS:204622

fi59g12.x1 (e-PCR)
- UniSTS:197758

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within auditory receptor cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within closure of optic fissure	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within fourth ventricle development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within glutamatergic neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within inner ear morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within midbrain-hindbrain boundary development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within optic cup morphogenesis involved in camera-type eye development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within otolith morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within podocyte development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within podocyte development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pronephric glomerulus morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within retina development in camera-type eye	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within semicircular canal morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: LIM homeobox transcription factor 1, beta b

Names: LIM homeobox transcription factor 1, beta 1; alo

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_001025167.2 → NP_001020338.2 LIM homeobox transcription factor 1, beta b

See identical proteins and their annotated locations for NP_001020338.2

Status: VALIDATED

Source sequence(s)

AY894989, BC162932, CR407581

UniProtKB/TrEMBL

B3DHY4, Q4L1M6, Q4VJ29

Related

ENSDARP00000070894.2, ENSDART00000076420.3

Conserved Domains (3) summary

cd09371
Location:33 → 85

LIM1_Lmx1b; The first LIM domain of Lmx1b

cd09378
Location:92 → 146

LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b

pfam00046
Location:197 → 250

Homeobox; Homeobox domain