MmuINT0008116 @ mm10
Intron Retention
Gene
ENSMUSG00000041797 | Abca9
Description
ATP-binding cassette, sub-family A (ABC1), member 9 [Source:MGI Symbol;Acc:MGI:2386796]
Coordinates
chr11:110144743-110145198:-
Coord C1 exon
chr11:110145079-110145198
Coord A exon
chr11:110144882-110145078
Coord C2 exon
chr11:110144743-110144881
Length
197 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
ACGTTTTCTCTGCTGTTCAGGTT
3' ss Score
8.85
Exon sequences
Seq C1 exon
GTACAACAAGTTCTACAGGACTTAGAAATGGAAAATATTCAAGACATTCTTGCTCAGAATTTAAGTGGCGGACAAAAAAGGAAGTTGACTCTTGGGATCGCCATTTTAGGAGACCCCCAG
Seq A exon
GTAAGTGGATAAAAATAACTCGTGACATCCAATCAGAGACTCAGAAACTAACATATTGGATAAATTTGCAAATGATACATTTAAGAAAACTTTTACATACGAATACCAATACCAATACTCTTACAACTACAGTATTTTCTAGAATCATCTTACGCCAGAGAAATAAATGGCCCTGTAACGTTTTCTCTGCTGTTCAG
Seq C2 exon
GTTTTGCTCCTGGATGAACCAACTGCTGGGTTGGATCCACTCTCGAGGCATCGCATATGGAACCTACTGAAAGAGAGGAGAGCAGGCAGAGTAATTGTCTTCAGTACTCAGTTCATGGATGAGGCTGATATCCTGGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041797:ENSMUST00000044850:14
Average complexity
IR
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:
PF0000522=ABC_tran=FE(26.5=100)
A:
NA
C2:
PF0000522=ABC_tran=PD(5.4=17.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAACAAGTTCTACAGGACTTAGA
R:
CGGCCAGGATATCAGCCTCAT
Band lengths:
257-454
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types