MmuINT0008113 @ mm9
Intron Retention
Gene
ENSMUSG00000041797 | Abca9
Description
ATP-binding cassette, sub-family A (ABC1), member 9 [Source:MGI Symbol;Acc:MGI:2386796]
Coordinates
chr11:110008222-110008587:-
Coord C1 exon
chr11:110008529-110008587
Coord A exon
chr11:110008333-110008528
Coord C2 exon
chr11:110008222-110008332
Length
196 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGA
5' ss Score
8.55
3' ss Seq
TATCTCTGCAATCATGTCAGGTC
3' ss Score
7.45
Exon sequences
Seq C1 exon
GATCAAAAATCTTAAAAAAGAATATTCTGGAAAGCATGGGAAAGTAGAAGCCTTGAGAG
Seq A exon
GTATGAAATAGGATTGCATTTAATGTGGGTGTGTGAGTTAGAGAATGAAGATGAGCGATTGTAGACACATTTTAAGGTTGCTCTTGTTTTTGAAGATTAGTACTCACACGCATATATGCAGTGAGAAACTGTAAGCTGTGGAGACTATAAAATGGTTATGCAAGTACTGAGTGTAATATCTCTGCAATCATGTCAG
Seq C2 exon
GTCTGGGGTTTGACATATATGAAGGCCAGATCACTGCCCTCCTTGGTCACAGTGGAGCTGGGAAAACCACCCTGATAAATACACTCAGTGGACTGTCACCCCCTACTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041797-Abca9:NM_147220:11
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=0.105
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=PU(1.4=9.5)
A:
NA
C2:
PF0000522=ABC_tran=FE(25.2=100)
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:
AAAAGAATATTCTGGAAAGCATGGGA
R:
TGTAGTAGGGGGTGACAGTCC
Band lengths:
154-350
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: