Scarletltr Gene Detail

Summary

• Symbol
  Scarletltr
• Name
  Scarletltr, erythroid developmental long intergenic non-protein coding transcript
• Synonyms
  2600006L11Rik

• Feature Type
  lncRNA gene
• IDs
  MGI:1924064
  NCBI Gene: 76814
• Alliance
  gene page
• Transcription Start Sites
  2 TSS

Location &
Maps

• Sequence Map
  Chr9:63988043-63994243 bp, + strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 9, 34.48 cM
• Mapping Data
  1 experiment

Strain
Comparison

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

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1924064	lncRNA gene	Chr9:63988043-63995327 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0015742	unclassified non-coding RNA gene	Chr9:63712732-63720152 (+)
A/J	MGP_AJ_G0015719	unclassified non-coding RNA gene	Chr9:61596618-61602798 (+)
AKR/J	MGP_AKRJ_G0015683	unclassified non-coding RNA gene	Chr9:63022725-63028919 (+)
BALB/cJ	MGP_BALBcJ_G0015680	unclassified non-coding RNA gene	Chr9:61320175-61327034 (+)
C3H/HeJ	MGP_C3HHeJ_G0015502	unclassified non-coding RNA gene	Chr9:63546486-63553913 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0016136	unclassified non-coding RNA gene	Chr9:65441727-65447926 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0013862	unclassified non-coding RNA gene	Chr9:61252843-61259384 (+)
CAST/EiJ	MGP_CASTEiJ_G0015057	unclassified non-coding RNA gene	Chr9:63707133-63714878 (+)
CBA/J	MGP_CBAJ_G0015482	unclassified non-coding RNA gene	Chr9:67702558-67711470 (+)
DBA/2J	MGP_DBA2J_G0015580	unclassified non-coding RNA gene	Chr9:61379933-61386233 (+)
FVB/NJ	MGP_FVBNJ_G0015585	unclassified non-coding RNA gene	Chr9:60680650-60687063 (+)
LP/J	MGP_LPJ_G0015660	unclassified non-coding RNA gene	Chr9:64008314-64015820 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0015608	unclassified non-coding RNA gene	Chr9:69005994-69012197 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0016178	unclassified non-coding RNA gene	Chr9:63133783-63141371 (+)
PWK/PhJ	MGP_PWKPhJ_G0014838	unclassified non-coding RNA gene	Chr9:61530991-61537168 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0014626	unclassified non-coding RNA gene	Chr9:63387884-63393880 (+)
WSB/EiJ	MGP_WSBEiJ_G0015161	unclassified non-coding RNA gene	Chr9:63032052-63038245 (+)

Homology

• Gene Tree
  Scarletltr
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  5 phenotype references
  

• All Mutations and Alleles
  4
• Chemically induced (other)
  1
• Gene trapped
  3
• Genomic Mutations
  1 involving Scarletltr
• Find Mice (IMSR)
  2 strains or lines available

Gene Ontology
(GO)
Classifications

Expression

• Assay Results
  706
• cDNA Data
  1

Tissue x Stage Matrix

• Other Mouse Links
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  23
• RefSeq
  1

• Ensembl
  ENSMUSG00000093759 (Evidence)
• NCBI Gene
  76814

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000093759	Ensembl Gene Model | MGI Sequence Detail	6201	C57BL/6J
transcript	ENSMUST00000176950	Ensembl | MGI Sequence Detail	305	Not Applicable

Molecular
Reagents

• All nucleic 1

  cDNA 1

References

• Summaries
  All 14

  Phenotypes 5
• Earliest
  J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
• Latest
  J:326411 Paralkar VR, et al., Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development. Blood. 2014 Mar 20;123(12):1927-37

TSS for Scarletltr:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr85588	Chr9:63992189-63992200 (+)	4,152 bp
Tssr85589	Chr9:63992201-63992218 (+)	4,167 bp