Sp9 MGI Mouse Gene Detail - MGI:3574660 - trans-acting transcription factor 9

Symbol

Sp9
Name

trans-acting transcription factor 9

Feature Type

protein coding gene
IDs

MGI:3574660
NCBI Gene: 381373
Alliance

genome feature page
Transcription Start Sites

7 TSS

Sequence Map

Chr2:73094809-73106115 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 43.52 cM
Mapping Data

1 experiment

SNPs within 2kb

193 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_3574660	protein coding gene	Chr2:73094809-73115050 (+)
129S1/SvImJ	ENSMUSG00200036071	protein coding gene	Chr2:70171048-70176594 (+)
A/J	ENSMUSG00195021095	protein coding gene	Chr2:70317634-70323180 (+)
AKR/J	ENSMUSG00220039144	protein coding gene	Chr2:70282240-70287788 (+)
BALB/cJ	ENSMUSG00180039787	protein coding gene	Chr2:70271408-70276954 (+)
C3H/HeJ	ENSMUSG00175033975	protein coding gene	Chr2:70386363-70391909 (+)
C57BL/6NJ	ENSMUSG00215019651	protein coding gene	Chr2:70213630-70219176 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0023656	protein coding gene	Chr2:67855319-67868049 (+)
CAST/EiJ	ENSTCUG00005008422	protein coding gene	Chr2:69711538-69717087 (+)
CBA/J	ENSMUSG00210032593	protein coding gene	Chr2:70429106-70434652 (+)
DBA/2J	ENSMUSG00185039605	protein coding gene	Chr2:70264891-70270437 (+)
FVB/NJ	ENSMUSG00205020460	protein coding gene	Chr2:69727693-69733237 (+)
JF1/MsJ	ENSUMUG00000006147	protein coding gene	Chr2:69925599-69931165 (+)
LP/J	ENSMUSG00230021263	protein coding gene	Chr2:72070751-72076297 (+)
NOD/ShiLtJ	ENSMUSG00190036056	protein coding gene	Chr2:70350388-70355932 (+)
NZO/HlLtJ	ENSMUSG00225014094	protein coding gene	Chr2:79814262-79819808 (+)
PWK/PhJ	ENSLUMG00010032247	protein coding gene	Chr2:70163546-70169117 (+)
SPRET/EiJ	ENSMSPG00010019357	protein coding gene	Chr2:71576324-71581868 (+)
WSB/EiJ	ENSIUOG00005018962	protein coding gene	Chr2:70393281-70398833 (+)

Human Ortholog

SP9, Sp9 transcription factor

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SP9, Sp9 transcription factor
Synonyms

ZNF990
Links

HGNC:30690

NCBI Gene ID: 100131390

UniProt: P0CG40
Chr Location

2q31.1; chr2:174334954-174338500 (+) GRCh38

MGI Vertebrate Homology

Sp9 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SP9
Gene Tree

Sp9

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Phenotype Summary

10 phenotypes from 2 alleles in 1 genetic background
2 phenotypes from multigenic genotypes
25 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

14
Chemically induced (other)

1
Endonuclease-mediated

2
Targeted

11
Genomic Mutations

7 involving Sp9
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

20 strains or lines available
Comparison Matrix

Gene Expression + Phenotype
Recombinase Activity

Comparison Matrix Gene Expression + Recombinase Activity

Mice homozygous for a knock-out allele fail to thrive and exhibit general weakness and postnatal lethality associated with striatum atrophy and loss of striatopallidal medium-sized spiny neurons (MSNs) due to decreased proliferation of striatopallidal MSN progenitors and increased apoptosis.

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All GO Annotations

9
GO References

6

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

654
Tissues

24
cDNA Data

10
Literature Summary

32

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

GEO

Expression Atlas
Other Vertebrate Links

Xenbase sp9

ZFIN sp9

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All Sequences

35
RefSeq

4
UniProt

1
CCDS

CCDS16126.1

Ensembl

ENSMUSG00000068859 (Evidence)
NCBI Gene

381373

			Length	Strain/Species	Flank
genomic	381373	NCBI Gene Model \| MGI Sequence Detail	11307	C57BL/6J	± kb
transcript	NM_001409583	RefSeq \| MGI Sequence Detail	3680	C57BL/6
polypeptide	Q64HY3	UniProt \| EBI \| MGI Sequence Detail	484	Not Applicable

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UniProt

1 Sequence
Protein Ontology

PR:000031727 transcription factor Sp9

(term hierarchy)
InterPro Domains

IPR036236 Zinc finger C2H2 superfamily

IPR013087 Zinc finger C2H2-type

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All nucleic 16

Genomic 1

cDNA 11

Primer pair 2

Other 2

Microarray probesets 1

Summaries

All 70

Developmental Gene Expression 32

Gene Ontology 6

Phenotypes 25
Earliest

J:95649 Kawakami Y, et al., Sp8 and Sp9, two closely related buttonhead-like transcription factors, regulate Fgf8 expression and limb outgrowth in vertebrate embryos. Development. 2004 Oct;131(19):4763-74
Latest

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

TSS for Sp9:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr18368	Chr2:73098341-73098349 (+)	3,536 bp
Tssr18369	Chr2:73102270-73102283 (+)	7,468 bp
Tssr18370	Chr2:73102291-73102303 (+)	7,488 bp
Tssr18371	Chr2:73104610-73104651 (+)	9,822 bp
Tssr18372	Chr2:73105057-73105069 (+)	10,254 bp
Tssr18373	Chr2:73105075-73105093 (+)	10,275 bp
Tssr18374	Chr2:73105143-73105152 (+)	10,339 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 09/08/2026 MGI 6.24