Halr1 Gene Detail

Summary

• Symbol
  Halr1
• Name
  Hoxa adjacent long noncoding RNA 1
• Synonyms
  Gm15055, Haunt, linc-Hoxa1, Linchoxa1

• Feature Type
  lncRNA gene
• IDs
  MGI:3705267
  NCBI Gene: 102635415
• Alliance
  genome feature page
• Transcription Start Sites
  2 TSS

Location &
Maps

• Sequence Map
  Chr6:52079929-52090664 bp, + strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 6, 25.40 cM

Strain
Comparison

• SNPs within 2kb
  401 from dbSNP Build 142
• Strain Annotations
  19

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_3705267	lncRNA gene	Chr6:52056776-52115615 (+)
129S1/SvImJ	ENSMUSG00200005644	lncRNA gene	Chr6:49057154-49069230 (+)
A/J	ENSMUSG00195007103	lncRNA gene	Chr6:48780960-48793054 (+)
AKR/J	ENSMUSG00220004026	lncRNA gene	Chr6:48490108-48502191 (+)
BALB/cJ	ENSMUSG00180027141	lncRNA gene	Chr6:49082685-49094768 (+)
C3H/HeJ	ENSMUSG00175017637	lncRNA gene	Chr6:48849255-48861346 (+)
C57BL/6NJ	ENSMUSG00215010817	lncRNA gene	Chr6:49033579-49045667 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0006344	lincRNA gene	Chr6:46587141-46597806 (+)
CAST/EiJ	ENSTCUG00005005263	lncRNA gene	Chr6:48340051-48352175 (+)
CBA/J	ENSMUSG00210018668	lncRNA gene	Chr6:48893541-48905634 (+)
DBA/2J	ENSMUSG00185013867	lncRNA gene	Chr6:49475805-49487894 (+)
FVB/NJ	ENSMUSG00205034802	lncRNA gene	Chr6:49133927-49146021 (+)
JF1/MsJ	ENSUMUG00000016433	lncRNA gene	Chr6:48848178-48860254 (+)
LP/J	ENSMUSG00230019701	lncRNA gene	Chr6:50554461-50566533 (+)
NOD/ShiLtJ	ENSMUSG00190036988	lncRNA gene	Chr6:48810524-48822595 (+)
NZO/HlLtJ	ENSMUSG00225013740	lncRNA gene	Chr6:52538363-52550454 (+)
PWK/PhJ	ENSLUMG00010022204	lncRNA gene	Chr6:48585449-48597504 (+)
SPRET/EiJ	ENSMSPG00010010564	lncRNA gene	Chr6:49169755-49181965 (+)
WSB/EiJ	ENSIUOG00005029073	lncRNA gene	Chr6:49155984-49168057 (+)

Homology

• Gene Tree
  Halr1
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  1 phenotype from 2 alleles in 2 genetic backgrounds
  8 phenotype references
  

• All Mutations and Alleles
  26
• Endonuclease-mediated
  1
• Gene trapped
  24
• Targeted
  1
• Find Mice (IMSR)
  30 strains or lines available

Mice homozygous for a null allele are viable.

Expression

• Assay Results
  598
• Tissues
  1
• cDNA Data
  1
• Literature Summary
  2

Images

Tissue x Stage Matrix

• Other Mouse Links
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  73
• RefSeq
  1

• Ensembl
  ENSMUSG00000085412 (Evidence)
• NCBI Gene
  102635415

Representative Sequences			Length	Strain/Species
genomic	102635415	NCBI Gene Model | MGI Sequence Detail	10736	C57BL/6J
transcript	NR_110440	RefSeq | MGI Sequence Detail	556	ZRU/MplStud

Molecular
Reagents

• All nucleic 1

  cDNA 1

References

• Summaries
  All 18

  Developmental Gene Expression 2

  Phenotypes 8
• Earliest
  J:86696 Zambrowicz BP, et al., Wnk1 kinase deficiency lowers blood pressure in mice: a gene-trap screen to identify potential targets for therapeutic intervention. Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):14109-14
• Latest
  J:330639 Han X, et al., Mouse knockout models reveal largely dispensable but context-dependent functions of lncRNAs during development. J Mol Cell Biol. 2018 Apr 1;10(2):175-178

TSS for Halr1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr56495	Chr6:52079916-52079935 (+)	-3 bp
Tssr56496	Chr6:52079941-52079968 (+)	26 bp