MmuINT0008040 @ mm9
Intron Retention
Gene
ENSMUSG00000041828 | Abca8a
Description
ATP-binding cassette, sub-family A (ABC1), member 8a [Source:MGI Symbol;Acc:MGI:2386846]
Coordinates
chr11:109930689-109931222:-
Coord C1 exon
chr11:109931103-109931222
Coord A exon
chr11:109930828-109931102
Coord C2 exon
chr11:109930689-109930827
Length
275 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
TCCTTTGATTCCTCCTCTAGATT
3' ss Score
9.96
Exon sequences
Seq C1 exon
GTACAAAGAGTTTTGCTGGAATTGGACATGAAAAATACTCAGAATATTCTTGTTCAAAACCTAAGCGGCGGACAGAAGAGAAAGCTGACGTTTGGAATCGCCATTTTAGGAGACCCTCAG
Seq A exon
GTAAGTCAGACTGCATTCATTGATAATTCAATCTGGAATCAAAGAATCTCCTCATCCAGAAAGGGCACTGTGATGGAGATCATACAGCGGAGGGGCCCATACAGCGGAGAGAACCATACCACGGAGGGAACCATACAGCGGAGGGGCCCATTCAGCGGAGGGAACCATACAGCGGAGGGGCCCATTCAGCGGAGCAGTAAACTAAGTGCATTCCTAGCCTCTGTGTTCCGTGCTCCCGAAGTTAGTGAGGTTATTTCCTTTGATTCCTCCTCTAG
Seq C2 exon
ATTTTCCTACTGGATGAGCCCACCGCTGGCCTGGATCCCTTTTCAAGGCACCGGGTGTGGAATTTCCTGAAGGAGCGCAGAGCAGACCGTGTGGTCCTCTTCAGCACGCAGTTCATGGATGAGGCTGACATCCTGGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041828-Abca8a:NM_153145:14
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=0.000
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
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAGTTTTGCTGGAATTGGACA
R:
AGCCAGGATGTCAGCCTCATC
Band lengths:
252-527
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: