MmuINT1009085 @ mm10
Intron Retention
Gene
ENSMUSG00000060461 | Dppa5a
Description
developmental pluripotency associated 5A [Source:MGI Symbol;Acc:MGI:101800]
Coordinates
chr9:78367721-78368177:-
Coord C1 exon
chr9:78367985-78368177
Coord A exon
chr9:78367904-78367984
Coord C2 exon
chr9:78367721-78367903
Length
81 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
CATTGCCTTTCCCCGGACAGGCC
3' ss Score
9.82
Exon sequences
Seq C1 exon
TCCTGAACCTGGAGCTGTGGGCCGTGCGTGGTGGATAAGCTTGATCTCGTCTTCCCTGAAGTCTGGTTCCTTGGCAGGATGATGGTGACCCTCGTGACCCGTAAAGATATCCCCCCGTGGGTGAAAGTTCCTGAAGACCTGAAAGATCCAGAAGTATTCCAGGTCCAGTCGCTGGTGCTGAAATATCTGTTTG
Seq A exon
GTGAGTAGCTACTCTTGACCTCGCTGCCAAGGCCCAAAGCTCCGGGTCTTGGAACTATGCTCATTGCCTTTCCCCGGACAG
Seq C2 exon
GCCCACAGGGATCTCGAATGTCTCACATCGAGCAGGTGAGCCAGGCCATGTTTGAGCTGAAGAACCTGGAATCTCCCGAAGAACTTATCGAGGTCTTCATTTACGGCTCTCAAAACAACAAGATTCGGGCTAAATGGATGCTTCAGTCCATGGCTGAGAGGTACCACCTGCGCCAGCAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000060461:ENSMUST00000071991:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0001324=KH_1=PU(23.8=38.5)
A:
NA
C2:
PF0001324=KH_1=PD(74.6=75.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCCTCGTGACCCGTAAAGAT
R:
TTCAGCTCAAACATGGCCTGG
Band lengths:
167-248
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types