Sox2ot MGI Mouse Gene Detail - MGI:2444112 - SOX2 overlapping transcript (non-protein coding)

Sequence Map

Chr3:34614530-34732142 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2444112	lncRNA gene	Chr3:34158419-34789489 (+)
129S1/SvImJ	ENSMUSG00200006430	lncRNA gene	Chr3:30891104-31469152 (+)
A/J	ENSMUSG00195001457	lncRNA gene	Chr3:30893343-31468436 (+)
AKR/J	ENSMUSG00220000914	lncRNA gene	Chr3:30927155-31506171 (+)
BALB/cJ	ENSMUSG00180002887	lncRNA gene	Chr3:31009854-31588737 (+)
C3H/HeJ	ENSMUSG00175003636	lncRNA gene	Chr3:30923680-31498691 (+)
C57BL/6NJ	ENSMUSG00215001617	lncRNA gene	Chr3:31283891-31862765 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0013631	unclassified non-coding RNA gene	Chr3:29033154-29603000 (+)
CAST/EiJ	ENSTCUG00005025733	lncRNA gene	Chr3:30778822-31353961 (+)
CBA/J	ENSMUSG00210002065	lncRNA gene	Chr3:30971928-31546914 (+)
DBA/2J	ENSMUSG00185001427	lncRNA gene	Chr3:31213161-31791994 (+)
FVB/NJ	ENSMUSG00205009264	lncRNA gene	Chr3:30386335-30971530 (+)
JF1/MsJ	ENSUMUG00000005757	lncRNA gene	Chr3:30651524-31235979 (+)
LP/J	ENSMUSG00230024131	lncRNA gene	Chr3:33134136-33712170 (+)
NOD/ShiLtJ	ENSMUSG00190001886	lncRNA gene	Chr3:31199981-31778809 (+)
NZO/HlLtJ	ENSMUSG00225007064	lncRNA gene	Chr3:35752116-36330207 (+)
PWK/PhJ	ENSLUMG00010037886	lncRNA gene	Chr3:30706810-31296636 (+)
SPRET/EiJ	ENSMSPG00010000757	lncRNA gene	Chr3:31087921-31671768 (+)
WSB/EiJ	ENSIUOG00005013932	lncRNA gene	Chr3:31206239-31792837 (+)

Vertebrate Orthology Source

Alliance of Genome Resources

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Phenotype Summary

1 phenotype from 1 allele in 1 genetic background
15 phenotype references

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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.

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Representative Sequences				Length	Strain/Species	Flank
	genomic	320478	NCBI Gene Model \| MGI Sequence Detail	117613	C57BL/6J	± kb
	transcript	NR_015580	RefSeq \| MGI Sequence Detail	2998	C57BL/6

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Summaries

All 38

Developmental Gene Expression 9

Diseases 1

Phenotypes 15
Earliest

J:93290 Araki K, et al., Exchangeable gene trap using the Cre/mutated lox system. Cell Mol Biol (Noisy-Le-Grand). 1999 Jul;45(5):737-50
Latest

J:366861 Como CN, et al., Meningeal-derived retinoic acid regulates neurogenesis via suppression of Notch and Sox2. Cell Rep. 2025 Apr 29;44(5):115637

Sox2ot expression regulated by:

Feature	Feature Type	Location	Reference
Rr297, regulatory region 297	promoter	Chr3:34614478-34614537	J:310878

TSS for Sox2ot:

(View these features in JBrowse)

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