lhx6a LIM homeobox 6a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: lhx6aprovided by ZNC
Official Full Name: LIM homeobox 6aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-041025-1
See related: Ensembl:ENSDARG00000006896 AllianceGenome:ZFIN:ZDB-GENE-041025-1
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: lhx6
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 forebrain neuron development and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of DNA-templated transcription. Predicted to be active in nucleus. Is expressed in forebrain; head mesenchyme; pharyngeal arch; and pharynx. Orthologous to human LHX6 (LIM homeobox 6). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 10

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	10	NC_007121.7 (9372702..9395220)
105	previous assembly	GRCz10 (GCF_000002035.5)	10	NC_007121.6 (9537480..9561661)

Chromosome 10 - NC_007121.7 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: 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?

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General gene information

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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
involved_in forebrain neuron development	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
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

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 protein Lhx6

Names: LIM homeobox 6

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_001004015.2 → NP_001004015.1 LIM/homeobox protein Lhx6

See identical proteins and their annotated locations for NP_001004015.1

Status: PROVISIONAL

Source sequence(s)

AY664403

UniProtKB/TrEMBL

B3DG01, F6P9A4, Q6BDC4

Related

ENSDARP00000017657.6, ENSDART00000021100.7

Conserved Domains (3) summary

cd09380
Location:97 → 150

LIM1_Lhx6; The first LIM domain of Lhx6

cd09382
Location:158 → 212

LIM2_Lhx6; The second LIM domain of Lhx6

pfam00046
Location:250 → 302

Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz11 Primary Assembly

Genomic

NC_007121.7 Reference GRCz11 Primary Assembly

Range

9372702..9395220

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_009305145.4 → XP_009303420.1 LIM/homeobox protein Lhx6 isoform X1

UniProtKB/TrEMBL

A0A8M3B623

Conserved Domains (3) summary

cd09380
Location:97 → 150

LIM1_Lhx6; The first LIM domain of Lhx6

cd09382
Location:157 → 211

LIM2_Lhx6; The second LIM domain of Lhx6

pfam00046
Location:249 → 301

Homeobox; Homeobox domain