Gm49580 Gene Detail

Summary

• Symbol
  Gm49580
• Name
  predicted gene, 49580

• Feature Type
  lncRNA gene
• IDs
  MGI:6214978
  NCBI Gene: 53960
• Alliance
  genome feature page
• Transcription Start Sites
  3 TSS

Location &
Maps

• Sequence Map
  Chr16:17846509-17849732 bp, + strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 16, 11.17 cM
• Mapping Data
  2 experiments

Strain
Comparison

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

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_6214978	lncRNA gene	Chr16:17846509-17849732 (+)
129S1/SvImJ	ENSMUSG00200046525	lncRNA gene	Chr16:14843091-14846293 (+)
A/J	ENSMUSG00195035745	lncRNA gene	Chr16:14400383-14403587 (+)
AKR/J	ENSMUSG00220046572	lncRNA gene	Chr16:14716662-14719866 (+)
BALB/cJ	ENSMUSG00180042670	lncRNA gene	Chr16:14641639-14644843 (+)
C3H/HeJ	ENSMUSG00175050093	lncRNA gene	Chr16:14786650-14789850 (+)
C57BL/6NJ	ENSMUSG00215043340	lncRNA gene	Chr16:14507753-14510957 (+)
CAROLI/EiJ	no annotation
CAST/EiJ	ENSTCUG00005045568	lncRNA gene	Chr16:14713367-14716610 (+)
CBA/J	ENSMUSG00210047113	lncRNA gene	Chr16:14802946-14806148 (+)
DBA/2J	ENSMUSG00185036455	lncRNA gene	Chr16:14749114-14752316 (+)
FVB/NJ	ENSMUSG00205048336	lncRNA gene	Chr16:14756732-14759936 (+)
JF1/MsJ	ENSUMUG00000054875	lncRNA gene	Chr16:14834672-14837828 (+)
LP/J	ENSMUSG00230046145	lncRNA gene	Chr16:17326964-17330162 (+)
NOD/ShiLtJ	ENSMUSG00190051475	lncRNA gene	Chr16:14889007-14892209 (+)
NZO/HlLtJ	ENSMUSG00225038171	lncRNA gene	Chr16:20572814-20576016 (+)
PWK/PhJ	ENSLUMG00010049096	lncRNA gene	Chr16:14713671-14716971 (+)
SPRET/EiJ	ENSMSPG00010048491	lncRNA gene	Chr16:14733503-14736119 (+)
WSB/EiJ	ENSIUOG00005045506	lncRNA gene	Chr16:14883289-14886491 (+)

Homology

• Gene Tree
  Gm49580
  

Human Diseases

• References
  3 with disease annotations

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  49 phenotype references
  

• All Mutations and Alleles
  6
• Endonuclease-mediated
  2
• Targeted
  4
• Genomic Mutations
  6 involving Gm49580
• Find Mice (IMSR)
  0 strains or lines available

Expression

• Assay Results
  597
• cDNA Data
  7

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  27
• RefSeq
  1
• UniProt
  1

• Ensembl
  ENSMUSG00000116658 (Evidence)
• NCBI Gene
  53960

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000116658	Ensembl Gene Model | MGI Sequence Detail	3224	C57BL/6J
transcript	ENSMUST00000232261	Ensembl | MGI Sequence Detail	1401	Not Applicable
polypeptide	Q3TTI1	UniProt | EBI | MGI Sequence Detail	66	Not Applicable

Protein
Information

• UniProt
  1 Sequence

Molecular
Reagents

• All nucleic 8

  Genomic 1

  cDNA 7

Other
Accession IDs

MGI:1858440

References

• Summaries
  All 58

  Diseases 3

  Phenotypes 49
• Earliest
  J:60871 Lund J, et al., Comparative sequence analysis of 634 kb of the mouse chromosome 16 region of conserved synteny with the human velocardiofacial syndrome region on chromosome 22q11.2. Genomics. 2000 Feb 1;63(3):374-83
• Latest
  J:389391 de Leon Reyes NS, et al., Interhemispheric CA1 projections to the subiculum support spatial cognition and are affected in a mouse model of the 22q11.2 deletion syndrome. Cell Rep. 2026 Mar 20;45(4):117114

TSS for Gm49580:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr137347	Chr16:17846521-17846526 (+)	15 bp
Tssr137348	Chr16:17846531-17846560 (+)	37 bp
Tssr137349	Chr16:17846575-17846577 (+)	67 bp