Hoxa11os MGI Mouse Gene Detail - MGI:107208 - homeobox A11, opposite strand

Symbol

Hoxa11os
Name

homeobox A11, opposite strand
Synonyms

Hoxa11as, Hoxa11os

Feature Type

lncRNA gene
IDs

MGI:107208
NCBI Gene: 15397
Alliance

genome feature page
Transcription Start Sites

2 TSS
Regulated by

Rr139 (1 regulatory region)

Sequence Map

Chr6:52222013-52226770 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 6, 25.40 cM

SNPs within 2kb

132 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_107208	lncRNA gene	Chr6:52220356-52226784 (+)
129S1/SvImJ	ENSMUSG00200005749	lncRNA gene	Chr6:49198655-49204063 (+)
A/J	ENSMUSG00195006935	lncRNA gene	Chr6:48922582-48927987 (+)
AKR/J	ENSMUSG00220004383	lncRNA gene	Chr6:48631665-48637073 (+)
BALB/cJ	ENSMUSG00180025704	lncRNA gene	Chr6:49224314-49229720 (+)
C3H/HeJ	ENSMUSG00175017431	lncRNA gene	Chr6:48990905-48996313 (+)
C57BL/6NJ	ENSMUSG00215011851	lncRNA gene	Chr6:49175148-49180554 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0013756	unclassified non-coding RNA gene	Chr6:46728045-46733458 (+)
CAST/EiJ	ENSTCUG00005005083	lncRNA gene	Chr6:48481297-48486705 (+)
CBA/J	ENSMUSG00210018449	lncRNA gene	Chr6:49035217-49040625 (+)
DBA/2J	ENSMUSG00185014050	lncRNA gene	Chr6:49617441-49622849 (+)
FVB/NJ	ENSMUSG00205028585	lncRNA gene	Chr6:49275539-49280945 (+)
JF1/MsJ	ENSUMUG00000015155	lncRNA gene	Chr6:48990263-48995666 (+)
LP/J	ENSMUSG00230019796	lncRNA gene	Chr6:50695945-50701353 (+)
NOD/ShiLtJ	ENSMUSG00190035840	lncRNA gene	Chr6:48952597-48958004 (+)
NZO/HlLtJ	ENSMUSG00225013849	lncRNA gene	Chr6:52679941-52685349 (+)
PWK/PhJ	ENSLUMG00010022388	lncRNA gene	Chr6:48727309-48732712 (+)
SPRET/EiJ	ENSMSPG00010010815	lncRNA gene	Chr6:49311179-49316592 (+)
WSB/EiJ	ENSIUOG00005029694	lncRNA gene	Chr6:49298009-49303416 (+)

Human Ortholog

HOXA11-AS, HOXA11 antisense RNA

Vertebrate Orthologs

1

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

HOXA11-AS, HOXA11 antisense RNA
Synonyms

HOXA11AS, HOXA11-AS1, HOXA11S, HOXA-AS5, LncHOXA11, NCRNA00076
Links

HGNC:24957

NCBI Gene ID: 221883
Chr Location

7p15.2; chr7:27184507-27189298 (+) GRCh38

MGI Vertebrate Homology

Hoxa11os stringent orthology
1 human;1 mouse
HCOP

vertebrate homology predictions: HOXA11-AS
Gene Tree

Hoxa11os

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Phenotype Summary

16 phenotypes from 1 allele in 1 genetic background
1 phenotype from multigenic genotypes
12 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

6
Endonuclease-mediated

1
Gene trapped

1
Targeted

4
Genomic Mutations

1 involving Hoxa11os
Find Mice (IMSR)

1 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele develop mild spontaneous intestinal inflammation as they age and show impaired mitochondrial OXPHOS in cells of the distal colon and increased susceptibility to experimental models of induced colitis.

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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

648
Tissues

36
cDNA Data

28
Literature Summary

10

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas

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All Sequences

45
RefSeq

1

Ensembl

ENSMUSG00000086427 (Evidence)
NCBI Gene

15397

Representative Sequences				Length	Strain/Species	Flank
	genomic	15397	NCBI Gene Model \| MGI Sequence Detail	4758	C57BL/6J	± kb
	transcript	NR_015348	RefSeq \| MGI Sequence Detail	1560	ZRU/MplStud

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All nucleic 32

cDNA 28

Primer pair 2

Other 2

Microarray probesets 4

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MGD-MRK-35670

Summaries

All 35

Developmental Gene Expression 10

Phenotypes 12
Earliest

J:25252 Hsieh-Li HM, et al., Hoxa 11 structure, extensive antisense transcription, and function in male and female fertility. Development. 1995 May;121(5):1373-85
Latest

J:344661 Shmuel-Galia L, et al., The lncRNA HOXA11os regulates mitochondrial function in myeloid cells to maintain intestinal homeostasis. Cell Metab. 2023 Aug 8;35(8):1441-1456.e9

Hoxa11os expression regulated by:

Feature	Feature Type	Location	Reference
Rr139, regulatory region 139	enhancer	Chr6, Syntenic	J:239414

TSS for Hoxa11os:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr56517	Chr6:52221981-52221994 (+)	-25 bp
Tssr56518	Chr6:52222004-52222019 (+)	-1 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