MmuINT0008096 @ mm10
Intron Retention
Gene
ENSMUSG00000020620 | Abca8b
Description
ATP-binding cassette, sub-family A (ABC1), member 8b [Source:MGI Symbol;Acc:MGI:1351668]
Coordinates
chr11:109940812-109941663:-
Coord C1 exon
chr11:109941546-109941663
Coord A exon
chr11:109940904-109941545
Coord C2 exon
chr11:109940812-109940903
Length
642 bp
Sequences
Splice sites
5' ss Seq
AAGGTTAGA
5' ss Score
6.12
3' ss Seq
ATATAATTCCTGTGTTTCAGGTG
3' ss Score
9.66
Exon sequences
Seq C1 exon
AAGCCAGTCATCATTGCCAGCTGCCTACGCAAAGAATATGCAGGGAAGCAGAAGCATTGCCTTTCCAAGAAGAAGGCCAAGATAGCCACTAGGAATGTCTCGTTTTGTGTCAGGAAAG
Seq A exon
GTTAGACATGTGGTTTTCAATAGTTGGCTCAAATAATGAAACTATTGAACTATTTCGTGGTTCTTGAGGAAAATCCTTCACACACTATCTTCTTACTCACGTGTGGACTCCTCTCCGGGTAGCCTGACAGCTCCTTTACACATTTCATTTTTAAGTACATACATTCACTCCAAGAATAGGGGCCCAGCTCTATCTACACAGGAACCAACACTACTATATGCCCCTTGAAAGCCATTACATTTTCTCTTAAACTCACACAACTGACATTCTAGTGTTTACGACTTTTAAAGAGAATTGGTTGGGGATGTAGCAGTATTTACTGAAGGCTTATGTTGGAGGAACTCAATTTTTAACATTACTACCAAAGACTTAAGGTCACAGGTAACAGAATCAGACACTCTTAGTTTCTAAGAATGGCTGTCCAATTTCCATTAGTATACTCTTGGGAAAATACCTCATTCTTGAGGCTTTTTATCACCAAGAATGAAAGAAGAGATTGTGATGATTTCTTGGGATAGTTGTGACAGTTAAATGGGACACACAAGGTACAAAACAATGACATACATCAGACAGTGAGAGTTAAGACTGTGCTATGCTTAGTTTTACTGTAAATTTACGTTCAATATAATTCCTGTGTTTCAG
Seq C2 exon
GTGAGATTCTAGGATTGTTGGGACACAATGGAGCTGGCAAAAGTACATCTCTTAAAATGATAAGTGGAGACACAAAAGTCACAGCTGGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020620:ENSMUST00000020948:30
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=0.032
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=PU(7.1=25.0)
A:
NA
C2:
PF0000522=ABC_tran=FE(21.3=100)
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:
AAGCCAGTCATCATTGCCAGC
R:
CTGCCCAGCTGTGACTTTTGT
Band lengths:
210-852
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