Haglr MGI Mouse Gene Detail - MGI:3026978 - Hoxd antisense growth associated long non-coding RNA

Symbol

Haglr
Name

Hoxd antisense growth associated long non-coding RNA
Synonyms

6720416L17Rik, Mdgt

Feature Type

bidirectional promoter lncRNA gene

BioType Conflict
IDs

MGI:3026978
NCBI Gene: 102634678
Alliance

genome feature page
Transcription Start Sites

3 TSS
Regulated by

Rr57 (1 regulatory region)

Sequence Map

Chr2:74578766-74593240 bp, - strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 44.13 cM
Mapping Data

2 experiments

SNPs within 2kb

360 from dbSNP Build 142
Strain Annotations

25

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_3026978	bidirectional promoter lncRNA gene	Chr2:74578766-74593293 (-)
129S1/SvImJ	ENSMUSG00200004055	lncRNA gene	Chr2:71627398-71641859 (-)
A/J	ENSMUSG00195019686	lncRNA gene	Chr2:71774124-71788587 (-)
A/J	ENSMUSG00195019328	protein coding gene	Chr2:71775556-71779747 (-)
AKR/J	ENSMUSG00220002245	protein coding gene	Chr2:71740183-71744374 (-)
AKR/J	ENSMUSG00220002589	lncRNA gene	Chr2:71738751-71753211 (-)
BALB/cJ	ENSMUSG00180007098	lncRNA gene	Chr2:71727779-71742239 (-)
C3H/HeJ	ENSMUSG00175011152	lncRNA gene	Chr2:71853648-71868165 (-)
C3H/HeJ	ENSMUSG00175010510	protein coding gene	Chr2:71855080-71859276 (-)
C57BL/6NJ	ENSMUSG00215030895	lncRNA gene	Chr2:71690610-71705087 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0005407	lincRNA gene	Chr2:69553097-69567393 (-)
CAST/EiJ	ENSTCUG00005031100	lncRNA gene	Chr2:71167567-71182073 (-)
CBA/J	ENSMUSG00210002527	lncRNA gene	Chr2:71896311-71910832 (-)
DBA/2J	ENSMUSG00185011558	lncRNA gene	Chr2:71732153-71746667 (-)
FVB/NJ	ENSMUSG00205020467	lncRNA gene	Chr2:71184160-71198618 (-)
FVB/NJ	ENSMUSG00205013682	protein coding gene	Chr2:71185592-71189781 (-)
JF1/MsJ	ENSUMUG00000044685	lncRNA gene	Chr2:71409047-71423575 (-)
LP/J	ENSMUSG00230026666	lncRNA gene	Chr2:73526994-73541457 (-)
LP/J	ENSMUSG00230024213	protein coding gene	Chr2:73528426-73532621 (-)
NOD/ShiLtJ	ENSMUSG00190009680	protein coding gene	Chr2:71808287-71812480 (-)
NOD/ShiLtJ	ENSMUSG00190010813	lncRNA gene	Chr2:71806855-71821315 (-)
NZO/HlLtJ	ENSMUSG00225015612	lncRNA gene	Chr2:81291059-81305538 (-)
PWK/PhJ	ENSLUMG00010032525	lncRNA gene	Chr2:71647397-71661862 (-)
SPRET/EiJ	ENSMSPG00010021470	lncRNA gene	Chr2:73047734-73062261 (-)
WSB/EiJ	ENSIUOG00005011673	lncRNA gene	Chr2:71850134-71864574 (-)

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Gene Tree

Haglr

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Phenotype Summary

3 phenotypes from 1 allele in 1 genetic background
39 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

16
Chemically induced (other)

1
Endonuclease-mediated

2
Radiation induced

1
Targeted

12
Genomic Mutations

15 involving Haglr
Find Mice (IMSR)

0 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a null mutation display partial penetrance of postnatal lethality and severe growth retardation.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

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

597
cDNA Data

4
Literature Summary

2

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas

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All Sequences

65
RefSeq

1
UniProt

1

Ensembl

ENSMUSG00000075277 (Evidence)
NCBI Gene

102634678

			Length	Strain/Species	Flank
genomic	102634678	NCBI Gene Model \| MGI Sequence Detail	14475	C57BL/6J	± kb
transcript	NR_110445	RefSeq \| MGI Sequence Detail	2454	C57BL/6
polypeptide	Q8BSK9	UniProt \| EBI \| MGI Sequence Detail	125	Not Applicable

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UniProt

1 Sequence

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All nucleic 4

cDNA 4

Microarray probesets 2

Summaries

All 53

Developmental Gene Expression 2

Phenotypes 39
Earliest

J:10491 Davisson MT, et al., The mouse mutation ulnaless on chromosome 2. J Hered. 1990 Mar-Apr;81(2):151-3
Latest

J:373797 Hintermann A, et al., Co-option of an ancestral cloacal regulatory landscape during digit evolution. Nature. 2025 Sep 17;

Haglr expression regulated by:

Feature	Feature Type	Location	Reference
Rr57, regulatory region 57	CpG island	Chr2:74593034-74594216	J:252916

TSS for Haglr:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr24631	Chr2:74583818-74583822 (-)	9,420 bp
Tssr24630	Chr2:74583799-74583807 (-)	9,437 bp
Tssr24629	Chr2:74583774-74583788 (-)	9,459 bp

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 09/15/2026 MGI 6.29