About   Help   FAQ
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
    gene page
  • Transcription Start Sites
    2 TSS
Location &
Maps
more
  • 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
more
  • SNPs within 2kb
    401 from dbSNP Build 142
  • Strain Annotations
    18
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_3705267
 lncRNA gene Chr6:52079903-52091977 (+)
129S1/SvImJ MGP_129S1SvImJ_G0006963
 lincRNA gene Chr6:51330142-51340773 (+)
A/J MGP_AJ_G0006958
 lincRNA gene Chr6:48937106-48947778 (+)
AKR/J MGP_AKRJ_G0006928
 lincRNA gene Chr6:50640230-50650896 (+)
BALB/cJ MGP_BALBcJ_G0006935
 lincRNA gene Chr6:49296529-49307247 (+)
C3H/HeJ MGP_C3HHeJ_G0006879
 lincRNA gene Chr6:50651290-50661945 (+)
C57BL/6NJ MGP_C57BL6NJ_G0007097
 lincRNA gene Chr6:52468715-52480770 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0006344
 lincRNA gene Chr6:46587141-46597806 (+)
CAST/EiJ MGP_CASTEiJ_G0006795
 lincRNA gene Chr6:50459131-50471332 (+)
CBA/J MGP_CBAJ_G0006861
 lincRNA gene Chr6:54654243-54667545 (+)
DBA/2J MGP_DBA2J_G0006881
 lincRNA gene Chr6:48860551-48871480 (+)
FVB/NJ MGP_FVBNJ_G0006904
 lincRNA gene Chr6:48471585-48482249 (+)
LP/J MGP_LPJ_G0006963
 lincRNA gene Chr6:51308392-51321670 (+)
NOD/ShiLtJ MGP_NODShiLtJ_G0006884
 lincRNA gene Chr6:57302154-57312952 (+)
NZO/HlLtJ MGP_NZOHlLtJ_G0007101
 lincRNA gene Chr6:50560804-50571575 (+)
PWK/PhJ MGP_PWKPhJ_G0006735
 lincRNA gene Chr6:48479677-48492256 (+)
SPRET/EiJ MGP_SPRETEiJ_G0006645
 lincRNA gene Chr6:49898896-49911986 (+)
WSB/EiJ MGP_WSBEiJ_G0006850
 lincRNA gene Chr6:50578715-50590246 (+)



Homology
less
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    1 phenotype from 2 alleles in 2 genetic backgrounds
    8 phenotype references
Mice homozygous for a null allele are viable.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    6
  • GO References
    2
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    707
  • Tissues
    1
  • cDNA Data
    1
  • Literature Summary
    2
Sequences &
Gene Models
less
  • All Sequences
    47
  • RefSeq
    1
Representative SequencesLengthStrain/SpeciesFlank
genomic 102635415 NCBI Gene Model | MGI Sequence Detail 10736 C57BL/6J ±  kb
transcript NR_110440 RefSeq | MGI Sequence Detail 556 ZRU/MplStud  
For the selected sequence
Molecular
Reagents
less
  • All nucleic 1
    cDNA 1
References
more
  • Summaries
    All 17
    Developmental Gene Expression 2
    Gene Ontology 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
Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources
Funding Information
Warranty Disclaimer, Privacy Notice, Licensing, & Copyright
Send questions and comments to User Support. 		last database update
11/12/2024
MGI 6.24 		The Jackson Laboratory