MmuINT0008058 @ mm10
Intron Retention
Gene
ENSMUSG00000041828 | Abca8a
Description
ATP-binding cassette, sub-family A (ABC1), member 8a [Source:MGI Symbol;Acc:MGI:2386846]
Coordinates
chr11:110036491-110038460:-
Coord C1 exon
chr11:110038343-110038460
Coord A exon
chr11:110036583-110038342
Coord C2 exon
chr11:110036491-110036582
Length
1760 bp
Sequences
Splice sites
5' ss Seq
AAGGTTGGA
5' ss Score
5.64
3' ss Seq
AGGTGTCTTCTTTTTCTCAGGTG
3' ss Score
8.96
Exon sequences
Seq C1 exon
AAGCCAGCCATCATTGCCAGCTGCCTTCGCAAGGAGTACAAGGGAAAGAAGAAATGCTTTGTTCTTAAGAGCAAGAAGAAGATTGCCACAAGAAACATCTCTTTTTGCGTTCGAAAAG
Seq A exon
GTTGGACACGGGTTCTGGCTCAGGAACATCCTCCAAGCTTTAGCGTCCCTGTCCTTCAGTCAGCATGCTCAGAAGCTATGTTGTTTCTTCGTTTCACAGTAGAGTGGCTGTTGACTGTTTCTCTCTGGACAGAAATGGTTTCCCCTTTGAGTAGGGGCATAGTCACACTGTTGTAAAAACCATAAACACACTTTGTCATTGAACCATTTAAAATACAGTCTTCCTATTCAATCAGTGCTGTTGCTCTCCTAATGATCAATACTGTTTACCAGGGAACTGACCTACATTCTGCTATTCCAACCTGATATCTTGACCACAGGGTAAGCGGAGCCTTGCCAACTTCTGACTCTCTCTGTCTGACGCAACAAGACTTAGTCTTTCCTCATCCTGTGGCTCTGGGCAAGTGGCTGAAACTCAAAAATTTCTATCCCTTTTCAGTGTTGTCACAGCTATTACCACTCCCCACACCATCATATAGTTTTCTTTAATTAACACATATTAATTGTACAGGCTAATGGGATTCACCCTGAGATTTCCATGCATGCAAATGTGGTATACCGATCATATTCAGCCACCCAGTTTCTCTCTGGCCCTCCACTCCCCACTTTGTCCACCATCTTTCCAGTATCAAGTAGTCCTTCCTTGGCTTTTTCTTTGTCTGTTTGTTTGTTTCATTTCTCAGCATCTTCAGTTTTTTCTCCACTATTCTGTAATTTTCACTATAAATTTTTTTCATCCACTTAGTTAGATTTATTGCTATATATCTTTTTTGCATACTTGTTGTGAATGGGTTTCTCTCTCAGTGTGTTCATATTGATGCATATCAATGCCATCTGGAGCTGAAGAGATTGTTTAAGACCAATTGCTCCTGCAGAGAACCTGCACTTGGTCACCAGTACCCACATGGTAGCTCATCACCATCAGTAGCTCCAGTTCTGAGGGATCTGACACCTCCTGACCTCTGCTGGCACCTGGGACTCGTGTGATACACAGGCATAAATGCATACAAAACACTCCTACAAAGAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAAATACATTTAAGAGCAGCTACCTGTTTTGTATGCTGGTTTCCTATCTTGCCACTCGCATCTTTCTGTGGACTTTTAAAAGATTTTCTACGTATAGAAGCATATTATTGCTAACAGAGATGATCCACTTGTCTACTTTCTTGTCCATAGATTTTTTTTTATTTCTTACATAATCGCTGTGTACTATATGGAGTAAGGGTGATAAAAGTGAACACCCAATCCTTTGCTTTATACCAGAGCCAAGTTTTTAATTTTCTTCATGAATCAGGATGTCTACTAAGGGCTTGTAATATGTAGTATTTTATCATGCCTGAACATGATCCTTTTAAAGATTTATTTTGCTTTTAACTATGCATTTTTTGTGTGGGGGTTTGTGCACTTGTGAGAGCAGATGTTTCCAGATCTAGATTAAGCACCAGGTCCCCAGGAGATGGAGTTTAAGAGATTATGAGATGCCTGCTATGGGTACTAAGAAGCAAGTTTAGGTCCTCTACAAGAACAATACACCCTCTCAGTGCTGAGCCATGTCTCGCCCTGTGTACTTTTACACCTATTTTATTTATGTCTCTTCACCTAACACGACAATTAAAATATAAAATCGTATTTAAGGCCCATTGTAAAGCACCTATCATACAGAGAAACCTATAATAGTCACTATCGTTACTAAGGTGTCTTCTTTTTCTCAG
Seq C2 exon
GTGAGGTTGTAGGATTACTGGGACACAATGGAGCTGGTAAAAGTACATCCATTAAGATGATAACTGGAGAAACCAAGCCAAGCGCCGGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041828:ENSMUST00000100287:30
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=0.204
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=PU(23.3=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:
AAGCCAGCCATCATTGCCAG
R:
CGCTTGGCTTGGTTTCTCCA
Band lengths:
202-1962
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