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
  11 TSS

Location &
Maps

• 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

• SNPs within 2kb
  442 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2444112	lncRNA gene	Chr3:34158419-34736768 (+)
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

• Human Ortholog
  SOX2-OT, SOX2 overlapping transcript

• Vertebrate Orthologs
  1

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  SOX2-OT, SOX2 overlapping transcript
  
• Synonyms
  NCRNA00043, SOX2OT
• Links
  HGNC:20209

  NCBI Gene ID: 347689

  
  
• Chr Location
  3q26.33; chr3:181056680-181742228 (+)  GRCh38.p7

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• Alliance of Genome Resources
  Sox2ot stringent orthology
  1 human;1 mouse
  
• HCOP
  vertebrate homology predictions: SOX2-OT
• Gene Tree
  Sox2ot
  

Human Diseases

• References
  1 with disease annotations

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  11 phenotype references
  

• All Mutations and Alleles
  108
• Gene trapped
  107
• Radiation induced
  1
• Genomic Mutations
  1 involving Sox2ot
• Find Mice (IMSR)
  4 strains or lines available

Expression

• Assay Results
  742
• Tissues
  25
• cDNA Data
  10
• Literature Summary
  8

Images

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  47
• RefSeq
  1

• Ensembl
  ENSMUSG00000105265 (Evidence)
• NCBI Gene
  320478

Representative Sequences			Length	Strain/Species
genomic	320478	NCBI Gene Model | MGI Sequence Detail	117613	C57BL/6J

Molecular
Reagents

• All nucleic 18

  cDNA 10

  Primer pair 6

  Other 2

  
  

  Microarray probesets 2

References

• Summaries
  All 33

  Developmental Gene Expression 8

  Diseases 1

  Phenotypes 11
• 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:310878 Li PY, et al., CRISPR/Cas9-mediated gene editing on Sox2ot promoter leads to its truncated expression and does not influence neural tube closure and embryonic development in mice. Biochem Biophys Res Commun. 2021 Oct 8;573:107-111

TSS for Sox2ot:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr28807	Chr3:34614343-34614352 (+)	-182 bp
Tssr28808	Chr3:34614361-34614373 (+)	-163 bp
Tssr28809	Chr3:34614493-34614499 (+)	-34 bp
Tssr28810	Chr3:34614509-34614535 (+)	-8 bp
Tssr28811	Chr3:34614775-34614795 (+)	255 bp
Tssr28812	Chr3:34615376-34615382 (+)	849 bp
Tssr28813	Chr3:34644066-34644103 (+)	29,555 bp
Tssr28814	Chr3:34644176-34644180 (+)	29,648 bp
Tssr28815	Chr3:34653958-34653965 (+)	39,432 bp
Tssr28819	Chr3:34694369-34694374 (+)	79,842 bp
Tssr28828	Chr3:34707735-34707742 (+)	93,209 bp