MmuINT0022838 @ mm9
Intron Retention
Gene
ENSMUSG00000027580 | BC006779
Description
cDNA sequence BC006779 [Source:MGI Symbol;Acc:MGI:2385169]
Coordinates
chr2:180963660-180964085:-
Coord C1 exon
chr2:180963929-180964085
Coord A exon
chr2:180963828-180963928
Coord C2 exon
chr2:180963660-180963827
Length
101 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
ATCTCCTCTCTGCCTCCCAGGGA
3' ss Score
9.39
Exon sequences
Seq C1 exon
GTCCGCATCATAAAGCAGTTGACCCTGGATCGGACGGTGGATCCCAAAGATATTGCTGTCCTTACACCCTACAATGCACAGGCTGCTGCAATCAGTAGGGGCCTCATGCAAAGAGGAGTCACCGGAGTGACTGTGACCTCTATTACCAAGAGCCAGG
Seq A exon
GTAAGGTTGGCTCTATGGGGCCATTTTTATGTGTGGGGTCAGCAGGAGGGGTCAGTGGGCAGAGCTGTGAATTCATCTATTATCTCCTCTCTGCCTCCCAG
Seq C2 exon
GGAGTGAGTGGCGCTATGTGATAGTGAGTACCGTCCGAACATGCCCCAGGAGTGATGTGGACCAGCGGCCAACAAAGAGCTGGCTCAAGAAGTTTCTGGGCTTTGTTGTGGACCCCCACCAAGTAAACGTGGCCATCACCCGGGCCCAGGAGGCGTTGTGCATCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027580-BC006779:NM_183162:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF130871=AAA_12=PD(9.3=45.5),PF130871=AAA_12=PU(25.0=90.9)
A:
NA
C2:
PF130871=AAA_12=FE(70.0=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:
AAAGCAGTTGACCCTGGATCG
R:
GCCCAGAAACTTCTTGAGCCA
Band lengths:
247-348
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: