Halr1 Hoxa adjacent long noncoding RNA 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Halr1provided by MGI
Official Full Name: Hoxa adjacent long noncoding RNA 1provided by MGI
Primary source: MGI:MGI:3705267
See related: AllianceGenome:MGI:3705267
Gene type: ncRNA
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Haunt; Gm15055; linc1547; Linchoxa1; linc-Evx1; linc-Hoxa1
Summary: Acts upstream of or within cellular response to retinoic acid and negative regulation of transcription by RNA polymerase II. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in kidney adult (RPKM 3.4), CNS E11.5 (RPKM 0.8) and 6 other tissues See more
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Genomic context

Location:: 6 B3; 6 25.4 cM

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (52079929..52090664)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (52102949..52113684)

Chromosome 6 - NC_000072.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The long noncoding RNA Gm15055 is highly expressed in mouse embryonic stem cells and its expression is maintained by OCT4.
Title: The long noncoding RNA Gm15055 represses Hoxa gene expression by recruiting PRC2 to the gene cluster.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1) 1 citation
Targeted (1) 1 citation

General gene information

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Other Names

long intergenic non-coding Hoxa1 regulatory RNA

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within cellular response to retinoic acid	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed

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.