MmuINT0022831 @ mm9
Intron Retention
Gene
ENSMUSG00000027580 | BC006779
Description
cDNA sequence BC006779 [Source:MGI Symbol;Acc:MGI:2385169]
Coordinates
chr2:180965713-180966207:-
Coord C1 exon
chr2:180965936-180966207
Coord A exon
chr2:180965845-180965935
Coord C2 exon
chr2:180965713-180965844
Length
91 bp
Sequences
Splice sites
5' ss Seq
AGGGTAGGT
5' ss Score
8.1
3' ss Seq
CACTCACACTCCTACCCCAGCAT
3' ss Score
3.8
Exon sequences
Seq C1 exon
CCGCAAGGAAGAAGCAGTGCGTCAACTGAAAACAGCATCCCCATTGGTCATTAGCATCGCCTTGGGCCTGCCTATCCCTGAGATCCGCTGGCCAATATCTGGGCCCCGTCGCTTAGTATCTGAGCTCCGTTGGCCAATACCCGGGCCCCGTCGCCCAGTATCTGAGCCCCATCGCCCAATGTCCGGGCCCTGTGGCCCAATATCTGAACCGTGTCGCTCAATCCCCGAGCCCTGCCGCGGCAACTGGCCTCGCCAGCATTCTTTTCACAAGG
Seq A exon
GTAGGTCTGCCCCTCAGCTTTTCCACCTCTCCCCAGCACCACGGTGCTCAGATGATCCTTGGCTTCTGCTACACTCACACTCCTACCCCAG
Seq C2 exon
CATCTACCAGCAGGTTCTTGGAGCGGCAGAACTACAACATCCCTGCTGGACATCATAAGCTGAACCAGAGCCAGGACAGGGCTGTCAGGAGCGCTCTGCAGAAACAGTTCACAGTCATCCAGGGCCCACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027580-BC006779:NM_183162:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.456 A=NA C2=0.689
Domain overlap (PFAM):
C1:
PF130861=AAA_11=PU(11.4=31.5)
A:
NA
C2:
PF130861=AAA_11=PU(10.0=55.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGAACCGTGTCGCTCAATC
R:
AACTGTTTCTGCAGAGCGCTC
Band lengths:
179-270
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: