MmuINT0022834 @ mm9
Intron Retention
Gene
ENSMUSG00000027580 | BC006779
Description
cDNA sequence BC006779 [Source:MGI Symbol;Acc:MGI:2385169]
Coordinates
chr2:180965039-180965385:-
Coord C1 exon
chr2:180965238-180965385
Coord A exon
chr2:180965156-180965237
Coord C2 exon
chr2:180965039-180965155
Length
82 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
ACCAAGGTCTTGCCTTCCAGGAG
3' ss Score
7.19
Exon sequences
Seq C1 exon
GACTGCTCCTGAGGAGGAAGACAGAGATGAAGCCCCTGCGTGTATATGGGGAGCAGGCAGAGGCCACTGAATTCCCGCTGCCAGGAGTGAGCAACAGGAGTCTGTTTGGCAAGACCTCTCAGGAAGGAAGACCAAATCAGAGCCTCAG
Seq A exon
GTATGGCCCCTTCTGTCTGTGCTGGGATTGAGGCCAAGGGGACCTCCACTGGCCAGGGTTTCACCAAGGTCTTGCCTTCCAG
Seq C2 exon
GAGCATTACCCTTCACCACCGGATCCGCCAGGCCCCCAACCCATATGCAGCAGAGATCAGAAAATTTGATGCCCAGCTTCGGGAAGGGAAAATATTCTCAAAGGAGGATCTTAGAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027580-BC006779:NM_183162:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.308 A=NA C2=0.127
Domain overlap (PFAM):
C1:
PF130861=AAA_11=FE(30.6=100)
A:
NA
C2:
PF130861=AAA_11=FE(15.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAGCCCCTGCGTGTATATGG
R:
CTCTGCTGCATATGGGTTGGG
Band lengths:
175-257
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: