MmuINT0023259 @ mm9
Intron Retention
Gene
ENSMUSG00000047228 | BC048546
Description
cDNA sequence BC048546 [Source:MGI Symbol;Acc:MGI:3039594]
Coordinates
chr6:128494943-128496478:-
Coord C1 exon
chr6:128496267-128496478
Coord A exon
chr6:128495153-128496266
Coord C2 exon
chr6:128494943-128495152
Length
1114 bp
Sequences
Splice sites
5' ss Seq
CAGGTGATT
5' ss Score
5.95
3' ss Seq
TATACCACTGTTCTGTTCAGGAC
3' ss Score
7.2
Exon sequences
Seq C1 exon
ATAATATGATATACTGGGAGAGAGATGAGAAACCCGAGACAGACAACTCTCCATCATTCATTCCTTCGGCACTTTCTGGTGAGACAGAGAAGACGTGCTATGTGCTGCTGGCTGTCCTTTCCCAGGACACTCAGGACCTTGATTATGCCAGCAAGATTGTGCAGTGGCTTGCCCAGCGGATGAACTCCCATGGAGGCTTCTCTGCCATGCAG
Seq A exon
GTGATTGGCTGAGACAGGGTGAATGTTTTTAATGCAGAGGATGACACTCCAGACGATAATCACAATTGTCACAATAACAGAGCTTCTGAGGTGAAAAGCATTAGATAACCTTTTTAAAGATGTATGCATTTTGCTTTGTGTATACGAATGTTTTGCACGTGTGTGCACCACATACATTGAATCACCTTGATCTGGAGTTAGAGATGCTCGTTAGCCACCCTGGGGGTGCTGGGAATCGAACCTAGGTCCTCTGCAAGAGCAACAGTGCTATTAACCATTGAGCCATGTCTCCAGCCCTCACATTTCATATTCTGAATCATACTCAGAATATTCACGGGCTCATCCTTGTGTTTCAGACACTCTTGCAAGGACACTCTATTTTAGGTGATAGATGAGAGTTTCCTTTTAAGGAATTTAGGCCAACTGTGTCTCCATTGCAGAGTAGAAAGCAGAATGGACGTCCAGAAGAGATTTTCTTCGTAAGAACAGAGTACTTAGATATCTGAATATCTATGATCTATGTACTGTAGATATCTGACGGTATAATGGTCAAAGCACTTGTCAATTTGGAATAGAGCTTCCTCTATGCTTCTGTGGTCTCTACATCAGAGAAAGCAAAAATGGGAACAGAAAACAAGAAAACGAATGGCCATGAAGCCATGGGTGATCCCTTCCCTAACAGGGAGAACTGAAAGTCAGGGGAAATAGAGTTTCATTTAATGAGGACAACCCCATTTTCTCTCCTCCTTTAAGGCTGAGTCCCCATGAGAGGGCAGGGTGATGAATTTCCAAAGACTCCTTTTTGATTTTTGTCCCTCTTTGAGAATAAGGAGACAGAAGTGTAGTCATCACACTGTGTGGTACCTTCACTTTCTGACTAGATTTGACATGATATCAGCAGTAGAGATGGTGATTTATTTTTTAAAAAATTTCAGAAAACTAAAATCCAATTAATTTGCTAAAGACAATGAACTGACAGCAACTCACACAACTAAGCACTCTCTGGTGTTTGTGGCATCAATTTGTGTCCTATTGGAAGCTTCAGGAATGTTTATGGAGACTGATGGAAAGTTCGTGGTCAACAATGGCTGACCTATACCACTGTTCTGTTCAG
Seq C2 exon
GACACCACAGTGTGCCTTCTCGCTCTAACCCAATACATGAAGTTAACCGGCTCTAACCCTCAAAACACCATCACGCTGAGCTCAGAGGAGTCTGAGGAGGTTTTCTATGTTAACAGAAATAAACGCCTTCTGGTCCAGCACTCAAAAGTATCCAAAGGCCACCAACAATACACAGTGGATGTAGAAGGAGATGGATGCTCATTTATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047228-BC048546:NM_001001179:29
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.197 A=NA C2=0.071
Domain overlap (PFAM):
C1:
PF076789=A2M_comp=FE(28.2=100)
A:
NA
C2:
PF076789=A2M_comp=PD(5.2=18.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCGAGACAGACAACTCTCCA
R:
CACTGTGTATTGTTGGTGGCCT
Band lengths:
357-1471
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: