MmuINT0008047 @ mm9
Intron Retention
Gene
ENSMUSG00000041828 | Abca8a
Description
ATP-binding cassette, sub-family A (ABC1), member 8a [Source:MGI Symbol;Acc:MGI:2386846]
Coordinates
chr11:109919738-109921360:-
Coord C1 exon
chr11:109921194-109921360
Coord A exon
chr11:109919872-109921193
Coord C2 exon
chr11:109919738-109919871
Length
1322 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAC
5' ss Score
7.82
3' ss Seq
CTTTTACATTTTACTACTAGGAG
3' ss Score
7.15
Exon sequences
Seq C1 exon
GATTCTGGTTTTGGGGATTGGACTTCTGCATATTTTGTCAGCAAATATTTACAGGATGGTCCGTCAAAGTGACTACTGTTGGGAGCTTGCCCCTCATATGTACTTCCTCACACCAGGCCAGCAACCACAGCCGCCCCTCACGAACTTACTGATCGTCAACAAAACAG
Seq A exon
GTAAACATGTTGCTAAACATGTGGTTTATGAATATTGTCACTGCTCAGAACATTGCTTAGGAAAGACACACATGACAGAAAGACGAATGTGCTTACATCCAGTTTAGGAAGCTCTATCTTAATTGAAACAACGAAGCCAAAAATATATGATAAAGGAGATATGTTTTATATCAGCACACATTAAAAAATTAAGGGTTATATAGAAATGTTGTGAAAATTGAATGTCACAATGATTATAAAGAGAGACTTGATAGTTGGGAAGAGGAGCACGTTGGTAGGCATACCTTTTAAATTTAAAAACATTTAAATTACATGATTACTATTGCTCCCATCAGTTCAACGGAATACGTTGTTTGATTCTAACAAGTTTTAGTCTAAAAGTCACAAGGTGTTAACAAAAGTTGTTTTTAATTATCAGAATTATTTTTAACTAGAAGAGATCATGAGCACATGAGAATTATTATCTTTATCAAACCATATTTAGATAGTCTATAAAAGAACAATTGAAGACTCAGCAAGAATTTTAATGGGTCAAGCACTTGGGGTGCAAGCATTGAGGACAGAGTTCAGATCCCCAGAGCCCACATAAAGATTTGTTGGTATGACCGACTTCTCTTCATGCAGCATCATATCTGTAAGCTAAAGTAAACACATACCCGCCCCGACATGTGCAAGTTGCTTTTGGTCCTGGTGTTTTATCATAGCAGTACAAAAATAGCTAAGATCCCATGATTCATTGGATGCCCCCATACCAGTTCTCATATGGGCAGCACTAACTGTACTCAATGGATTATAAAGAAACAAAGTCCAGAACTGGGGAAGGTGTCAAGGTAGGAGGTGTGGCTGATAGAAGTTAGGAGAAGCAGTGGTGAGTGGAAATATGACCAAGGCAGATTCTATGCATATTTGAAATTCTTAAATAACTAATAAAAATGCGGGCTTAAAAAAAGCTTAGTGAATATGGAGACCTATGTGTAATCCTAGAAATGGGTACTCAGAGCAGCTGGCCAAATAGACTGAGTTGGTGAGCTCTAGCCTAAGGGAAAAACCCTGGTTCAATATGTACAGTGAAGAGTGATGACAGAGATCTTTGGCCTCCACATGCTTGTGTATGCATGTGCTCTTGCACGAATAATAGCATGCGCACATGCACATAAATAAAAAAGGGAACAAAAGGTATTTGTTCAGAAAAGAAATATATGGAGAATTAAAATCCATACTATTGCATGCTGTAACAATCAAATGACTGTGAAGAGTCATTTTGATACATAATTTTGTAGTGTTCTTTTGGATTTATAGTGCCTTTTACATTTTACTACTAG
Seq C2 exon
GAGCAAAAATCGATGACTTTATACATTCACTGGAACAACAGAACATAGCTTTGGAAGTTGATGCCTTTGGGACTAGAAATGGCACCGAGGACAGTCAGTATAATGGAGCTATCATCCTATCAGGTGACGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041828-Abca8a:NM_153145:20
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(15.8=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(12.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGGTTTTGGGGATTGGACT
R:
TCGTCACCTGATAGGATGATAGCT
Band lengths:
294-1616
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: