Rubie Gene Detail

Summary

• Symbol
  Rubie
• Name
  RNA upstream of Bmp4 expressed in inner ear
• Synonyms
  Gm15219

• Feature Type
  lncRNA gene
• IDs
  MGI:5568573
  NCBI Gene: 100873094
• Alliance
  genome feature page
• Transcription Start Sites
  1 TSS

Location &
Maps

• Sequence Map
  Chr14:46805788-46813308 bp, - strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 14, 24.11 cM

Strain
Comparison

• SNPs within 2kb
  305 from dbSNP Build 142
• Strain Annotations
  19

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_5568573	lncRNA gene	Chr14:46805720-46835882 (-)
129S1/SvImJ	ENSMUSG00200016965	lncRNA gene	Chr14:35595793-35625971 (-)
A/J	ENSMUSG00195026329	lncRNA gene	Chr14:35824498-35854668 (-)
AKR/J	ENSMUSG00220038718	lncRNA gene	Chr14:35198631-35228797 (-)
BALB/cJ	ENSMUSG00180044327	lncRNA gene	Chr14:35428175-35458349 (-)
C3H/HeJ	ENSMUSG00175028918	lncRNA gene	Chr14:37113895-37144067 (-)
C57BL/6NJ	ENSMUSG00215038597	lncRNA gene	Chr14:35825691-35855851 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0005033	lincRNA gene	Chr14:38430476-38436367 (-)
CAST/EiJ	ENSTCUG00005010837	lncRNA gene	Chr14:37613972-37643864 (-)
CBA/J	ENSMUSG00210042948	lncRNA gene	Chr14:35759162-35789332 (-)
DBA/2J	ENSMUSG00185015244	lncRNA gene	Chr14:40548314-40578140 (-)
FVB/NJ	ENSMUSG00205047545	lncRNA gene	Chr14:34986470-35016305 (-)
JF1/MsJ	ENSUMUG00000049689	lncRNA gene	Chr14:52601329-52631451 (-)
LP/J	ENSMUSG00230021720	lncRNA gene	Chr14:52819070-52848864 (-)
NOD/ShiLtJ	ENSMUSG00190038995	lncRNA gene	Chr14:35451205-35481035 (-)
NZO/HlLtJ	ENSMUSG00225050975	lncRNA gene	Chr14:43063202-43093005 (-)
PWK/PhJ	ENSLUMG00010039773	lncRNA gene	Chr14:35050042-35080050 (-)
SPRET/EiJ	ENSMSPG00010003081	lncRNA gene	Chr14:38375140-38404718 (-)
WSB/EiJ	ENSIUOG00005042692	lncRNA gene	Chr14:35327463-35357322 (-)

Homology

• Gene Tree
  Rubie
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  5 phenotypes from 2 alleles in 2 genetic backgrounds
  4 phenotype references
  

• All Mutations and Alleles
  3
• Chemically induced (other)
  1
• Endonuclease-mediated
  1
• Spontaneous
  1
• Genomic Mutations
  1 involving Rubie
• Find Mice (IMSR)
  0 strains or lines available
• Comparison Matrix
  Gene Expression + Phenotype

Mice homozygous for a spontaneous retroviral insertion that is SWR-specific exhibit hyperactivity, bidirectional circling, and abnormal lateral semicircular canal formation. Mice homozygous for a null allele exhibit circling.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  1
• GO References
  1

Expression

• Assay Results
  633
• Tissues
  14
• cDNA Data
  2
• Literature Summary
  2

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

• Other Mouse Links
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  27
• RefSeq
  1

• Ensembl
  ENSMUSG00000085123 (Evidence)
• NCBI Gene
  100873094

Representative Sequences			Length	Strain/Species
genomic	100873094	NCBI Gene Model | MGI Sequence Detail	7521	C57BL/6J
transcript	NR_046459	RefSeq | MGI Sequence Detail	1404	C57BL/6

Molecular
Reagents

• All nucleic 10

  cDNA 2

  Primer pair 8

Other
Accession IDs

MGI:3705294

References

• Summaries
  All 10

  Developmental Gene Expression 2

  Gene Ontology 1

  Phenotypes 4
• Earliest
  J:209710 Roberts KA, et al., Mutation of Rubie, a novel long non-coding RNA located upstream of Bmp4, causes vestibular malformation in mice. PLoS One. 2012;7(1):e29495
• Latest
  J:284183 George MR, et al., Minimal in vivo requirements for developmentally regulated cardiac long intergenic non-coding RNAs. Development. 2019 Dec 9;146(23):dev185314

TSS for Rubie:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr128285	Chr14:46813306-46813312 (-)	-1 bp