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
  genome feature page
• Transcription Start Sites
  2 TSS

Location &
Maps

• Sequence Map
  Chr9:63988043-63995327 bp, + strand

  From NCBI 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
  273 from dbSNP Build 142
• Strain Annotations
  19

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1924064	lncRNA gene	Chr9:63945709-63996045 (+)
129S1/SvImJ	ENSMUSG00200043400	lncRNA gene	Chr9:61090607-61096801 (+)
A/J	ENSMUSG00195026453	lncRNA gene	Chr9:60800252-60806447 (+)
AKR/J	ENSMUSG00220043339	lncRNA gene	Chr9:60950637-60956831 (+)
BALB/cJ	ENSMUSG00180018256	lncRNA gene	Chr9:60938270-60944470 (+)
C3H/HeJ	ENSMUSG00175012878	lncRNA gene	Chr9:60934047-60940242 (+)
C57BL/6NJ	ENSMUSG00215034562	lncRNA gene	Chr9:60925386-60931587 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0013862	unclassified non-coding RNA gene	Chr9:61252843-61259384 (+)
CAST/EiJ	ENSTCUG00005034486	lncRNA gene	Chr9:60846599-60852744 (+)
CBA/J	ENSMUSG00210014409	lncRNA gene	Chr9:61021459-61027655 (+)
DBA/2J	ENSMUSG00185036048	lncRNA gene	Chr9:61044667-61050864 (+)
FVB/NJ	ENSMUSG00205033263	lncRNA gene	Chr9:61370886-61377081 (+)
JF1/MsJ	ENSUMUG00000038180	lncRNA gene	Chr9:61108316-61114472 (+)
LP/J	ENSMUSG00230039728	lncRNA gene	Chr9:61289782-61295977 (+)
NOD/ShiLtJ	ENSMUSG00190022538	lncRNA gene	Chr9:61130255-61136467 (+)
NZO/HlLtJ	ENSMUSG00225046741	lncRNA gene	Chr9:61355093-61361289 (+)
PWK/PhJ	ENSLUMG00010027521	lncRNA gene	Chr9:61073125-61079281 (+)
SPRET/EiJ	ENSMSPG00010023059	lncRNA gene	Chr9:62133634-62139767 (+)
WSB/EiJ	ENSIUOG00005027319	lncRNA gene	Chr9:60536773-60542966 (+)

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
  597
• cDNA Data
  1

Tissue x Stage Matrix

• Other Mouse Links
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  35
• RefSeq
  1

• Ensembl
  ENSMUSG00000093759 (Evidence)
• NCBI Gene
  76814

Representative Sequences			Length	Strain/Species
genomic	76814	NCBI Gene Model | MGI Sequence Detail	7285	C57BL/6J
transcript	NR_040743	RefSeq | MGI Sequence Detail	316	C57BL/6

Molecular
Reagents

• All nucleic 1

  cDNA 1

References

• Summaries
  All 15

  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