lmx1a LIM homeobox transcription factor 1, alpha [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: lmx1aprovided by ZNC
Official Full Name: LIM homeobox transcription factor 1, alphaprovided by ZNC
Primary source: ZFIN:ZDB-GENE-041014-332
See related: Ensembl:ENSDARG00000020354 AllianceGenome:ZFIN:ZDB-GENE-041014-332
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: si:ch211-260g14.3
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 neuron differentiation and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of transcription, DNA-templated. Predicted to be active in nucleus. Is expressed in brain; cranial ganglion; and otic vesicle. Human ortholog(s) of this gene implicated in autosomal dominant nonsyndromic deafness 7. Orthologous to human LMX1A (LIM homeobox transcription factor 1 alpha). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 20

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	20	NC_007131.7 (33921847..33940264)
105	previous assembly	GRCz10 (GCF_000002035.5)	20	NC_007131.6 (34019460..34037384)

Chromosome 20 - NC_007131.7 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
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 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 transcription factor 1-alpha; LIM homeobox transcription factor 1, alpha

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_001025498.1 → NP_001020669.1 LIM homeobox transcription factor 1-alpha

Status: PROVISIONAL

Source sequence(s)

BX296562

UniProtKB/TrEMBL

A0A8M1N746, Q5RI65

Related

ENSDARP00000006532.7, ENSDART00000019059.9

Conserved Domains (3) summary

cd09370
Location:26 → 77

LIM1_Lmx1a; The first LIM domain of Lmx1a

pfam00046
Location:188 → 241

Homeobox; Homeobox domain

cl02475
Location:84 → 140

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007131.7 Reference GRCz11 Primary Assembly

Range

33921847..33940264

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021468445.1 → XP_021324120.1 LIM homeobox transcription factor 1, alpha isoform X1

UniProtKB/TrEMBL

A0A8M9PSR7

Conserved Domains (3) summary

cd09370
Location:7 → 58

LIM1_Lmx1a; The first LIM domain of Lmx1a

cl02475
Location:65 → 121

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

pfam00046
Location:169 → 222

Homeobox; Homeobox domain
XM_005160713.3 → XP_005160770.1 LIM homeobox transcription factor 1, alpha isoform X2

See identical proteins and their annotated locations for XP_005160770.1

UniProtKB/TrEMBL

A0A8M2B7U0

Conserved Domains (1) summary

pfam00046
Location:90 → 143

Homeobox; Homeobox domain
XM_005160714.3 → XP_005160771.1 LIM homeobox transcription factor 1, alpha isoform X2

See identical proteins and their annotated locations for XP_005160771.1

UniProtKB/TrEMBL

A0A8M2B7U0

Conserved Domains (1) summary

pfam00046
Location:90 → 143

Homeobox; Homeobox domain