Six6 MGI Mouse Gene Detail - MGI:1341840 - sine oculis-related homeobox 6

Symbol

Six6
Name

sine oculis-related homeobox 6
Synonyms

Optx2, Six9

Feature Type

protein coding gene
IDs

MGI:1341840
NCBI Gene: 20476
Alliance

gene page
Transcription Start Sites

5 TSS

Sequence Map

Chr12:72986666-72991673 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 12, 30.31 cM
Mapping Data

2 experiments

SNPs within 2kb

155 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1341840	protein coding gene	Chr12:72986656-72991673 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0019831	protein coding gene	Chr12:72807171-72812182 (+)
A/J	MGP_AJ_G0019789	protein coding gene	Chr12:70097916-70102914 (+)
AKR/J	MGP_AKRJ_G0019764	protein coding gene	Chr12:72217777-72222784 (+)
BALB/cJ	MGP_BALBcJ_G0019769	protein coding gene	Chr12:70573174-70578172 (+)
C3H/HeJ	MGP_C3HHeJ_G0019574	protein coding gene	Chr12:72645966-72650964 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0020221	protein coding gene	Chr12:75078098-75083105 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0017839	protein coding gene	Chr12:67552226-67557227 (+)
CAST/EiJ	MGP_CASTEiJ_G0019126	protein coding gene	Chr12:67434953-67439956 (+)
CBA/J	MGP_CBAJ_G0019544	protein coding gene	Chr12:77918150-77923148 (+)
DBA/2J	MGP_DBA2J_G0019660	protein coding gene	Chr12:69982857-69987864 (+)
FVB/NJ	MGP_FVBNJ_G0019647	protein coding gene	Chr12:68843358-68848365 (+)
LP/J	MGP_LPJ_G0019732	protein coding gene	Chr12:72836424-72841431 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0019686	protein coding gene	Chr12:81092373-81097368 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0020256	protein coding gene	Chr12:71693861-71698868 (+)
PWK/PhJ	MGP_PWKPhJ_G0018891	protein coding gene	Chr12:64294299-64299322 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0018686	protein coding gene	Chr12:66108058-66113059 (+)
WSB/EiJ	MGP_WSBEiJ_G0019177	protein coding gene	Chr12:72290791-72295798 (+)

Human Ortholog

SIX6, SIX homeobox 6

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SIX6, SIX homeobox 6
Synonyms

MCOPCT2, ODRMD, OPTX2, Six9
Links

HGNC:10892

NCBI Gene ID: 4990

neXtProt AC: NX_O95475

UniProt: O95475
Chr Location

14q23.1; chr14:60509146-60512850 (+) GRCh38

MGI Vertebrate Homology

Six6 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: SIX6
Gene Tree

Six6

Diseases

1 with human SIX6 associations

				Human Disease	Mouse Models
				optic disc anomalies with retinal and/or macular dystrophy IDs optic disc anomalies with retinal and/or macular dystrophy DOID:0080635 OMIM:212550

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

27 phenotypes from 1 allele in 2 genetic backgrounds
15 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

5
Chemically induced (other)

1
Targeted

4
Genomic Mutations

1 involving Six6
Incidental Mutations

APF
Find Mice (IMSR)

16 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for disruptions in this gene display retinal and pituitary gland hypoplasia, hypothalamic dysregulation, and reduced male and female fertility.

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All GO Annotations

12
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

1115
Tissues

224
cDNA Data

30
Literature Summary

56

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

Xenbase six6

ZFIN six6a, six6b

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All Sequences

35
RefSeq

2
UniProt

2
CCDS

CCDS25972.1

Ensembl

ENSMUSG00000021099 (Evidence)
NCBI Gene

20476

			Length	Strain/Species	Flank
genomic	ENSMUSG00000021099	Ensembl Gene Model \| MGI Sequence Detail	5008	C57BL/6J	± kb
transcript	ENSMUST00000021519	Ensembl \| MGI Sequence Detail	4009	Not Applicable
polypeptide	ENSMUSP00000021519	Ensembl \| MGI Sequence Detail	246	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000014901 homeobox protein SIX6

(term hierarchy)
InterPro Domains

IPR001356 Homeobox domain

IPR009057 Homeobox-like domain superfamily

IPR031701 Homeobox protein SIX1, N-terminal SD domain

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All nucleic 43

cDNA 32

Primer pair 8

Other 3

Microarray probesets 4

Summaries

All 93

Developmental Gene Expression 56

Gene Ontology 6

Phenotypes 15
Earliest

J:55598 Toy J, et al., The optx2 homeobox gene is expressed in early precursors of the eye and activates retina-specific genes. Proc Natl Acad Sci U S A. 1998 Sep 1;95(18):10643-8
Latest

J:357477 Ferrena A, et al., Six3 and Six6 jointly control diverse target genes in multiple cell populations over developmental trajectories of mouse embryonic retinal progenitor cells. PLoS One. 2024;19(10):e0308839

TSS for Six6:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr113767	Chr12:72986503-72986532 (+)	-148 bp
Tssr113768	Chr12:72986648-72986662 (+)	-11 bp
Tssr3858	Chr12:72986665-72986674 (+)	4 bp
Tssr113769	Chr12:72986682-72986703 (+)	27 bp
Tssr113770	Chr12:72986712-72986715 (+)	48 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 12/10/2024 MGI 6.24