MmuINT0022837 @ mm9
Intron Retention
Gene
ENSMUSG00000027580 | BC006779
Description
cDNA sequence BC006779 [Source:MGI Symbol;Acc:MGI:2385169]
Coordinates
chr2:180963929-180964614:-
Coord C1 exon
chr2:180964261-180964614
Coord A exon
chr2:180964086-180964260
Coord C2 exon
chr2:180963929-180964085
Length
175 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
CTGCCCTCTTATCTACTTAGGTC
3' ss Score
10.4
Exon sequences
Seq C1 exon
GTGGTTCTGCTTGGAGACCACAAGCAGCTTCGGCCTGTGGTCAAGAGTGAACAGCTGCAGAGTCTGGGGATGGATCGGTCTCTCTTTGAGAGGTACCACAGGGATGCCATCATGCTGGACACACAGTACCGTATGCATAAGGACATCTGTTCCTTCCCCTCCGTGGAGTTCTATGGGGGAAAGCTAAAGACCTGGTCTGACCTGAGGCGTCTGCCTAGTATCCTGGGTCACACTGGCAAGCCGAGCTGTTCCGTCATCTTCGGCTCTGTGCAGGGCCATGAGCAGAAGCTGCTGGTGTCCACCGAGGATGGCAATGAGAACTCTAGGGCCAACCCAGAGGAAGTCACACAGGTG
Seq A exon
GTAAGTGTCAGAGTGACTCTCCATGGTGTTTGGTGGGTCAGGGAAGGCTTCCTGGAGGAGGGTGAAGGCCAAGGAAAGCTTCACTGGATGGGAAGGCTGGTATTGAGTGAGGTTGCTGAGCTCAGAAAAGAACAGGGTCTGGGTTCCAGCTCCGTCTGCCCTCTTATCTACTTAG
Seq C2 exon
GTCCGCATCATAAAGCAGTTGACCCTGGATCGGACGGTGGATCCCAAAGATATTGCTGTCCTTACACCCTACAATGCACAGGCTGCTGCAATCAGTAGGGGCCTCATGCAAAGAGGAGTCACCGGAGTGACTGTGACCTCTATTACCAAGAGCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027580-BC006779:NM_183162:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.145 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF130861=AAA_11=PD(6.4=13.6),PF130871=AAA_12=PU(45.4=79.7)
A:
NA
C2:
PF130871=AAA_12=PD(9.3=45.5),PF130871=AAA_12=PU(25.0=90.9)
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:
TATCCTGGGTCACACTGGCAA
R:
CTTTGCATGAGGCCCCTACTG
Band lengths:
249-424
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: