MmuINT0008050 @ mm9
Intron Retention
Gene
ENSMUSG00000041828 | Abca8a
Description
ATP-binding cassette, sub-family A (ABC1), member 8a [Source:MGI Symbol;Acc:MGI:2386846]
Coordinates
chr11:109915797-109917732:-
Coord C1 exon
chr11:109917625-109917732
Coord A exon
chr11:109915971-109917624
Coord C2 exon
chr11:109915797-109915970
Length
1654 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGTA
5' ss Score
5.69
3' ss Seq
TGATTGTACTTCCTTACCAGAAC
3' ss Score
7.16
Exon sequences
Seq C1 exon
GAAAATGACCACAGAAAATTTGATTATTTGGCTTATTTCTTCTTGTGGGTACTTCTGATGGCCTGTGTTCCTCCTTATATTTCCATGACCAGCATTGATGACTATAAG
Seq A exon
GTAGTAAAAAAAAAAATTAATGGAAACTAAAGTTGATTTAAACAATCAGAAGTTGTTTATAATGTGATTGCAGGGTTTCTCGTTACTATGGTGTGCAGTTTTATACACTGAGCAGTTGATTAATACACAATTGCACCTTTATAGAAGTAAAAAGGAAGAATGCACTAAAGGAAAGGAAAAGGAAGGAGGTGGGGAGGACAAGTGGAAAGACCATGAGAAAGGAAAATAAGAGAAAGATTAAAAAGCTTTGTTTGTTTCCTTCTAAAGAATGGAGGCATTGGGATAAAGATTGAACACTTCCCCAAATGTAATCTTTTCAGTGGAAGATGGGTGAGATTCCATATAAAAATTTGAGTTGTATATCACACATATCTTCTTGGAACTAGCTCATGGAACACAAAGAGGTCTTGAGCAGCACCCCAAGGTCTTAATAAACTAAAAGAAGAACCTGGAATCCTAAAGGGTGGAGTGGCTGGAATCTGCCTCTAAGCATTCTGTCAGTGCAGGAATTACCTAGAGCAAGGGCAGTAGACCTCTACTCAAGGGTAGCTTACACTATGTTGCCAAGACGAAGCATGGAGTAGAACTTCATGATGTCACGACTGTACAGATGTCTGTAAGAAGAGCACATTCAGAAGTTATATAGGATTGGTACCTGCTTCCAGTCATCAGTTATAGGGGTTACCCCAAGGATCCAAATTTGGGGCAAGACTTGATCAATTAAGAACAGACCCAGAAATGACAAAGGAAATGAAAGAAGTAACAAATAGGAAAAGTTAACACAATCAAGGATTAACTAAAAGAATGAACACAATGAAGAGAGAAAACACACACACACACACACACACACACACATACACACATGTCAGGTGGAACTCCTAATGTAGCTATATAAAAAAAATGAACATGGCTTTTAGAACAGACATACAGTTAAAACAGAATGAACCAGAATAGACAGTAAAATTGAAACACAGAAAGAAAGAAAAAACGCTCTGAAAAATTATCTGAACTTTAATGATTCATGAGACAATAGTAATGACTCATCATATATTTAATTAGAATTTCTAAGGCAGAGAAGAGCTAGAAATGACAGAAAATACACTTGGAAAAAACAAAATTTTTATCATTTGGCAGATTTTTAAAATATAAAATTTAGTGAAACATAAAATAACTACACATATGAAATACATTAATGGCTTTAAATATGAGAAACTCCAAAGCTATCAAAGTACCACACAAGGTGCAATTACTAACAGTGTTTTAATCACTCATTTTCATTGAGAATAAACCAATATGACAATTTTACGTGGAAAAAAAATGGCTACTTTCATTTGGATAAGGGATGAATTGTTTTACCACTGAAAGCTAATACTCACATGGGGAATTTTCCTTTGTAGGCATTAAGTCAATCTTTGGCTAACTGCCTTATTGCTGTCAGTAACTTGGATGGTTTATTTTATTAGCTACGTTATCACATTAGGTTAAATTATTTTTATTAGTAACAACAGCAAATTTTGATATAGAAGCTTTGAAATGACCCATGTCCCTTCTTCTGTGTAGTGTTTAATCACTAATAATGAATAACTCATTTGGTTATTTTCTTCATATTTTTATAAAAAACAATATACAATTGATGATTGTACTTCCTTACCAG
Seq C2 exon
AACAGAGCTCAGTTCCAGCTGTGGATTTCAGGGCTCTCCCCATCTGCATACTGGTTCGGGCAGGCTCTGTTTGAGGTTCCAGTGTACTGTGCACTCATTTTGTCTATATTCATTGCATTCTATGCCTCGGCCCCTCCAGAGAGTAAGTTCACAGTTGGAGATCTGTTTATTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041828-Abca8a:NM_153145:23
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:
PF126982=ABC2_membrane_3=FE(9.9=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(16.1=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:
GACCACAGAAAATTTGATTATTTGGC
R:
AAACAGATCTCCAACTGTGAACT
Band lengths:
270-1924
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: