MmuINT0022836 @ mm9
Intron Retention
Gene
ENSMUSG00000027580 | BC006779
Description
cDNA sequence BC006779 [Source:MGI Symbol;Acc:MGI:2385169]
Coordinates
chr2:180964261-180964967:-
Coord C1 exon
chr2:180964772-180964967
Coord A exon
chr2:180964615-180964771
Coord C2 exon
chr2:180964261-180964614
Length
157 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
ATAGCTATCTGTGCCTCTAGGTG
3' ss Score
8.64
Exon sequences
Seq C1 exon
GTACAGGAGAGTCTTGGGGAAGGCACGCAAACATGAACTGGAGCGGCACTCGGTCATCCTGTGCACGTGCTCCTGTGCGGCATCAAAGAGCCTGAAAATTCTGAATGTTCGACAGATCCTTATCGACGAGGCAGGCATGGCCACTGAGCCAGAGACCCTTATCCCCTTGGTGTGCTTCTCAAAGACGGTTGAGAAG
Seq A exon
GTGAGGGTTGTGGGGATCTAGTGCTCCTGCCTGGATTCCTGGGGGCAGCTGATGTTGGGGTGCTAAGGGTGTAATAGGTGAGCATTGAAGATGGCCAAGAAGTTGGAATGCTTCTGGCTCCAAAGATGTCAAAATCAATAGCTATCTGTGCCTCTAG
Seq C2 exon
GTGGTTCTGCTTGGAGACCACAAGCAGCTTCGGCCTGTGGTCAAGAGTGAACAGCTGCAGAGTCTGGGGATGGATCGGTCTCTCTTTGAGAGGTACCACAGGGATGCCATCATGCTGGACACACAGTACCGTATGCATAAGGACATCTGTTCCTTCCCCTCCGTGGAGTTCTATGGGGGAAAGCTAAAGACCTGGTCTGACCTGAGGCGTCTGCCTAGTATCCTGGGTCACACTGGCAAGCCGAGCTGTTCCGTCATCTTCGGCTCTGTGCAGGGCCATGAGCAGAAGCTGCTGGTGTCCACCGAGGATGGCAATGAGAACTCTAGGGCCAACCCAGAGGAAGTCACACAGGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027580-BC006779:NM_183162:15
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=0.145
Domain overlap (PFAM):
C1:
PF130861=AAA_11=FE(26.0=100)
A:
NA
C2:
PF130861=AAA_11=PD(6.4=13.6),PF130871=AAA_12=PU(45.4=79.7)
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:
GCCAGAGACCCTTATCCCCTT
R:
CCTCAGGTCAGACCAGGTCTT
Band lengths:
256-413
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: