About   Help   FAQ
Sox2ot Gene Detail
Summary
  • Symbol
    Sox2ot
  • Name
    SOX2 overlapping transcript (non-protein coding)
  • Synonyms
    B230215L15Rik
  • Feature Type
    lncRNA gene
  • IDs
    MGI:2444112
    NCBI Gene: 320478
  • Alliance
    gene page
  • Transcription Start Sites
    8 TSS
  • Regulated by
    Rr297 (1 regulatory region)
Location &
Maps
more
  • Sequence Map
    Chr3:34614530-34732142 bp, + strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 3, 16.56 cM
  • Mapping Data
    2 experiments
Strain
Comparison
more
  • SNPs within 2kb
    2703 from dbSNP Build 142
  • Strain Annotations
    18
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_2444112
 lncRNA gene Chr3:34158419-34789489 (+)
129S1/SvImJ MGP_129S1SvImJ_G0015499
 unclassified non-coding RNA gene Chr3:31750992-32364628 (+)
A/J MGP_AJ_G0015476
 unclassified non-coding RNA gene Chr3:31264426-31832952 (+)
AKR/J MGP_AKRJ_G0015440
 unclassified non-coding RNA gene Chr3:31790554-32385100 (+)
BALB/cJ MGP_BALBcJ_G0015439
 unclassified non-coding RNA gene Chr3:30907507-31492604 (+)
C3H/HeJ MGP_C3HHeJ_G0015262
 unclassified non-coding RNA gene Chr3:31836382-32426893 (+)
C57BL/6NJ MGP_C57BL6NJ_G0015893
 unclassified non-coding RNA gene Chr3:33335829-33954829 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0013631
 unclassified non-coding RNA gene Chr3:29033154-29603000 (+)
CAST/EiJ MGP_CASTEiJ_G0014814
 unclassified non-coding RNA gene Chr3:31666010-32276893 (+)
CBA/J MGP_CBAJ_G0015243
 unclassified non-coding RNA gene Chr3:34206066-34845395 (+)
DBA/2J MGP_DBA2J_G0015337
 unclassified non-coding RNA gene Chr3:30738409-31313391 (+)
FVB/NJ MGP_FVBNJ_G0015344
 unclassified non-coding RNA gene Chr3:30186173-30767377 (+)
LP/J MGP_LPJ_G0015415
 unclassified non-coding RNA gene Chr3:32530574-33151265 (+)
NOD/ShiLtJ MGP_NODShiLtJ_G0015368
 unclassified non-coding RNA gene Chr3:36714592-37332508 (+)
NZO/HlLtJ MGP_NZOHlLtJ_G0015933
 unclassified non-coding RNA gene Chr3:31588315-32175445 (+)
PWK/PhJ MGP_PWKPhJ_G0014602
 unclassified non-coding RNA gene Chr3:30291281-30891154 (+)
SPRET/EiJ MGP_SPRETEiJ_G0014390
 unclassified non-coding RNA gene Chr3:30986937-31591495 (+)
WSB/EiJ MGP_WSBEiJ_G0014921
 unclassified non-coding RNA gene Chr3:31603797-32214117 (+)



Homology
more
  • Human Ortholog
    SOX2-OT, SOX2 overlapping transcript
  • Vertebrate Orthologs
    2
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    SOX2-OT, SOX2 overlapping transcript
  • Synonyms
    NCRNA00043, SOX2OT
  • Links
    NCBI Gene ID: 347689

  • Chr Location
    3q26.33; chr3:180989510-181836880 (+)  GRCh38
Human Diseases
less
  • References
    1 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    1 phenotype from 1 allele in 1 genetic background
    13 phenotype references
Gene Ontology
(GO)
Classifications
less
Molecular Function

No experimental evidence to support Molecular Function annotation, following literature review. See J:73796.
Biological Process

No experimental evidence to support Biological Process annotation, following literature review. See J:73796.
Cellular Component

No experimental evidence to support Cellular Component annotation, following literature review. See J:73796.
Expression
less
Expression Overview

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
    805
  • Tissues
    27
  • cDNA Data
    10
  • Literature Summary
    9
Sequences &
Gene Models
less
  • All Sequences
    135
  • RefSeq
    1
Representative SequencesLengthStrain/SpeciesFlank
genomic 320478 NCBI Gene Model | MGI Sequence Detail 117613 C57BL/6J ±  kb
transcript NR_015580 RefSeq | MGI Sequence Detail 2998 C57BL/6  
For the selected sequence
Molecular
Reagents
less
  • All nucleic 22
    cDNA 10
    Primer pair 10
    Other 2

    Microarray probesets 2
References
more
  • Summaries
    All 36
    Developmental Gene Expression 9
    Diseases 1
    Phenotypes 13
  • 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
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
03/25/2025
MGI 6.24 		The Jackson Laboratory