Hoxb9 MGI Mouse Gene Detail - MGI:96190

Symbol

Hoxb9
Name

homeobox B9
Synonyms

Hox-2.5

Feature Type

protein coding gene
IDs

MGI:96190
NCBI Gene: 15417
Member of

Hoxb cluster
Alliance

genome feature page
Transcription Start Sites

8 TSS
Regulated by

Rr36, Rr578 (2 regulatory regions)

Sequence Map

Chr11:96162283-96167421 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 11, 59.81 cM
Mapping Data

9 experiments

SNPs within 2kb

143 from dbSNP Build 142
Strain Annotations

19
PCR

2

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_96190	protein coding gene	Chr11:96162156-96167421 (+)
129S1/SvImJ	ENSMUSG00200049414	protein coding gene	Chr11:93406651-93411791 (+)
A/J	ENSMUSG00195047555	protein coding gene	Chr11:93128304-93133466 (+)
AKR/J	ENSMUSG00220044426	protein coding gene	Chr11:93387384-93392545 (+)
BALB/cJ	ENSMUSG00180046068	protein coding gene	Chr11:93391521-93396665 (+)
C3H/HeJ	ENSMUSG00175048953	protein coding gene	Chr11:93387382-93392521 (+)
C57BL/6NJ	ENSMUSG00215053818	protein coding gene	Chr11:92979803-92984944 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0017024	protein coding gene	Chr11:92042738-92047909 (+)
CAST/EiJ	ENSTCUG00005045306	protein coding gene	Chr11:92830468-92835619 (+)
CBA/J	ENSMUSG00210051524	protein coding gene	Chr11:93090822-93095992 (+)
DBA/2J	ENSMUSG00185049207	protein coding gene	Chr11:93437223-93442363 (+)
FVB/NJ	ENSMUSG00205025474	protein coding gene	Chr11:93293706-93298848 (+)
JF1/MsJ	ENSUMUG00000050112	protein coding gene	Chr11:93743431-93748603 (+)
LP/J	ENSMUSG00230045934	protein coding gene	Chr11:94489735-94494873 (+)
NOD/ShiLtJ	ENSMUSG00190045936	protein coding gene	Chr11:93485180-93490322 (+)
NZO/HlLtJ	ENSMUSG00225049653	protein coding gene	Chr11:96545523-96550661 (+)
PWK/PhJ	ENSLUMG00010050551	protein coding gene	Chr11:93288590-93293728 (+)
SPRET/EiJ	ENSMSPG00010046303	protein coding gene	Chr11:93790573-93794178 (+)
WSB/EiJ	ENSIUOG00005046415	protein coding gene	Chr11:93232879-93238029 (+)

Human Ortholog

HOXB9, homeobox B9

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

HOXB9, homeobox B9
Synonyms

HOX2, HOX-2.5, HOX2E
Links

HGNC:5120

NCBI Gene ID: 3219

UniProt: P17482
Chr Location

17q21.32; chr17:48621156-48626358 (-) GRCh38

MGI Vertebrate Homology

Hoxb9 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: HOXB9
Protein SuperFamily

Homeobox_Hox9
Gene Tree

Hoxb9

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Phenotype Summary

7 phenotypes from 1 allele in 1 genetic background
17 phenotypes from multigenic genotypes
22 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

7
Endonuclease-mediated

1
Gene trapped

1
Targeted

5
Genomic Mutations

3 involving Hoxb9
Incidental Mutations

APF
Find Mice (IMSR)

12 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mutations affect developing thoracic skeletal elements. Homozygotes exhibit rib fusion, abnormal rib attachment to the sternum, and reduced intercostal segments of the sternum. Homozygotes or heterozygotes may show an eighth rib attached to the sternum.

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All GO Annotations

51
GO References

13

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.

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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

912
Tissues

201
cDNA Data

17
Literature Summary

77

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA HOXB9

Xenbase hoxb9

ZFIN hoxb9a

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All Sequences

40
RefSeq

2
UniProt

4
CCDS

CCDS25292.1

Ensembl

ENSMUSG00000020875 (Evidence)
NCBI Gene

15417

			Length	Strain/Species	Flank
genomic	ENSMUSG00000020875	Ensembl Gene Model \| MGI Sequence Detail	5139	C57BL/6J	± kb
transcript	ENSMUST00000000010	Ensembl \| MGI Sequence Detail	2574	Not Applicable
polypeptide	ENSMUSP00000000010	Ensembl \| MGI Sequence Detail	250	Not Applicable

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UniProt

4 Sequences
Protein Ontology

PR:000008706 homeobox protein Hox-B9

(term hierarchy)
InterPro Domains

IPR017970 Homeobox, conserved site

IPR017112 Homeobox protein HXA9/HXB9/HXC9

IPR001356 Homeodomain

IPR009057 Homeodomain-like superfamily

IPR020479 Homeodomain, metazoa

IPR006711 Hox9, N-terminal activation domain

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All nucleic 73

Genomic 18

cDNA 21

Primer pair 14

Other 20

Microarray probesets 3

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MGD-MRK-10833, MGD-MRK-10891

Summaries

All 140

Developmental Gene Expression 77

Gene Ontology 13

Phenotypes 22
Earliest

J:9628 Do MS, et al., Gene organization of murine homeobox-containing gene clusters. Genomics. 1988 Oct;3(3):195-200
Latest

J:388827 Chen Y, et al., Gastrula-Premarked Posterior Enhancer Primes Posterior Tissue Development Through Cross-Talk with TGF-beta Signaling Pathway. Adv Sci (Weinh). 2025 Sep;12(36):e00895

Hoxb9 expression regulated by:

Feature	Feature Type	Location	Reference
Rr36, regulatory region 36	response element	Chr11:96201561-96201577	J:336097
Rr578, regulatory region 578	response element	Chr11:96215137-96215156	J:336097

TSS for Hoxb9:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr104449	Chr11:96161968-96161979 (+)	-309 bp
Tssr104450	Chr11:96162035-96162050 (+)	-240 bp
Tssr104451	Chr11:96162056-96162065 (+)	-222 bp
Tssr104452	Chr11:96162149-96162164 (+)	-126 bp
Tssr104453	Chr11:96162279-96162308 (+)	11 bp
Tssr104454	Chr11:96162442-96162483 (+)	180 bp
Tssr104455	Chr11:96162743-96162759 (+)	468 bp
Tssr104456	Chr11:96162761-96162787 (+)	491 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)
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