lhx1a LIM homeobox 1a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: lhx1aprovided by ZNC
Official Full Name: LIM homeobox 1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-347
See related: Ensembl:ENSDARG00000014018 AllianceGenome:ZFIN:ZDB-GENE-980526-347
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: LHX1; lim1; wu:fe25d04; wu:fj36b06
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. Predicted to be involved in several processes, including embryonic morphogenesis; generation of neurons; and kidney development. Predicted to act upstream of or within regulation of DNA-templated transcription. Predicted to be part of protein-containing complex. Predicted to be active in nucleus. Is expressed in several structures, including germ ring; mesoderm; nervous system; neural rod; and renal system. Orthologous to human LHX1 (LIM homeobox 1). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 15

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	15	NC_007126.7 (27703060..27711021, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	15	NC_007126.6 (27770533..27777477, complement)

Chromosome 15 - NC_007126.7 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
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?

Inactivation of either PINCH isoform independently leads to instability of ILK, loss of stretch-responsive anf and vegf expression, and progressive heart failure
Title: PINCH proteins regulate cardiac contractility by modulating integrin-linked kinase-protein kinase B signaling.

Submit: New GeneRIF Correction

General gene information

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Markers

lim1 (e-PCR)
- UniSTS:205577

fj36b06.x1 (e-PCR)
- UniSTS:188473

lim1 (e-PCR)
- UniSTS:186984

lim1 (e-PCR)
- UniSTS:238281

fe25d04.x1 (e-PCR)
- UniSTS:196334

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	ISS Inferred from Sequence or Structural Similarity 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
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in S-shaped body morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in anterior/posterior axis specification	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell-cell signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in cerebellar Purkinje cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in cerebellar Purkinje cell-granule cell precursor cell signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in cerebellum development	ISS Inferred from Sequence or Structural Similarity more info
involved_in comma-shaped body morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in dorsal spinal cord interneuron posterior axon guidance	ISS Inferred from Sequence or Structural Similarity more info
involved_in dorsal/ventral pattern formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in ectoderm formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in embryonic pattern specification	ISS Inferred from Sequence or Structural Similarity more info
involved_in embryonic retina morphogenesis in camera-type eye	ISS Inferred from Sequence or Structural Similarity more info
involved_in endoderm formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in forebrain regionalization	ISS Inferred from Sequence or Structural Similarity more info
involved_in gastrulation with mouth forming second	ISS Inferred from Sequence or Structural Similarity more info
involved_in lateral motor column neuron migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in motor neuron axon guidance	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in nephric duct morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in paramesonephric duct development	ISS Inferred from Sequence or Structural Similarity more info
involved_in pattern specification process	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of anterior head development	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of branching involved in ureteric bud morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of embryonic development	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of gastrulation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of nephron tubule epithelial cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in post-embryonic development	ISS Inferred from Sequence or Structural Similarity more info
involved_in primitive streak formation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in renal vesicle morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in retina layer formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in spinal cord association neuron differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in ureteric bud development	ISS Inferred from Sequence or Structural Similarity more info
involved_in urogenital system development	ISS Inferred from Sequence or Structural Similarity more info

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
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
part_of protein-containing complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: LIM/homeobox protein Lhx1

Names: LIM homeobox protein 1; homeobox protein Lim-1; lim1a

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_131216.1 → NP_571291.1 LIM/homeobox protein Lhx1

See identical proteins and their annotated locations for NP_571291.1

Status: PROVISIONAL

Source sequence(s)

L37802

UniProtKB/Swiss-Prot

Q90476

UniProtKB/TrEMBL

B3DGH2

Related

ENSDARP00000021069.5, ENSDART00000005641.6

Conserved Domains (3) summary

cd09367
Location:4 → 55

LIM1_Lhx1_Lhx5; The first LIM domain of Lhx1 (also known as Lim1) and Lhx5

cd09375
Location:63 → 118

LIM2_Lhx1_Lhx5; The second LIM domain of Lhx1 (also known as Lim1) and Lhx5

pfam00046
Location:182 → 235

Homeobox; Homeobox domain