MmuINT0008074 @ mm9
Intron Retention
Gene
ENSMUSG00000020620 | Abca8b
Description
ATP-binding cassette, sub-family A (ABC1), member 8b [Source:MGI Symbol;Acc:MGI:1351668]
Coordinates
chr11:109831132-109833167:-
Coord C1 exon
chr11:109832999-109833167
Coord A exon
chr11:109831191-109832998
Coord C2 exon
chr11:109831132-109831190
Length
1808 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACA
5' ss Score
8.88
3' ss Seq
ATGCTTTTTCTCTTTTGCAGAAT
3' ss Score
11.98
Exon sequences
Seq C1 exon
ATGAATACGGACATCAGCACTCTCCCCTGTTTTTCCTGAAATCTTCATTTTGGCTACAAACACGAAAGCCTGCTCATGTGATTCTTGAAGATGGAATAGACCCCGTTCCTTCATCAGGTGACTCGTTTGAACCGGTGTCCCCAGAATTCCACGGGAAAGAATCCATCAG
Seq A exon
GTAACAAGGATGAGAACAGAGACACCGCTAAGACAGAGGAAGTTCAAATTTTAGCATTGAAAGCAAGCAAAGCACTCGTTAGGGCCTCTAGATAGTCAGGGGTGTCTCCGCCCAGCGATCTACACTAACTTGCACTGGAAGGATAAAGAAAAACTCATTCAAGAGATCCTTTCTGTCTCTGTCTGTCTGTCTGTCTGTCTGTCTCCCTTCCTCCTTCCCTCCCTTCCTCTCTCACTTCCTCCCTCTTTCCCTCCCTCCCTCTTTCCCTCCCTCCCTCTTTCCCTCCCTCCCTCCTTCTCTCCCTCCTCTCAAAACTGGAACTCAAACCTCCGGCTTTGCACATGCTAGACACCACTATATCACTGAGATACATCCTCCACCCATTTTTAACTTTTTAATTCTTGAGACAGGGCTTCACTAAGTTGTCCTTGATTTTACTCTGTAGCCCAGGCAGGCTTTCAGCTTGCAACCCGACAGCTTCCACGTCCAAGATAGCTGGGGTAAGAGGTTTGCCCCATCAGCTTCAGGTCTAGTTACCACACACACACACACACACACACACACACACACTCACGTGCACACAAAGTAGGGAGGAAGGAAAAGGAGAAGCTGTAGAGACAGACACAAGAGGCACACAGGAAGCTGTGTCCCTCAGAGTGTGGCAGCACATTGTCTACTTCCCAATAAGAAAACAGGAGCAAGTCCTCAGGTTGCCAATGTCACCTCCCCCCGCCCCCCCCAGTGACATCTCCCACCAGCCCTTTGATGTCTCATCCCTTGACCCTCTGAGCTCCCAAAGCCCACTGCATTCTGTTCTCACCAGTGCCCTATGCTGCTATTTGTCCTGGAACCTAAGGAAGCCAAGAAAAACAACTTCCCCACAAAATTCGTTTCTTTATTTTCTTTTCTTGTGTATCTCTTCAGCACCACTTGCCAAGTGTGAGGACCTTGAACTGGCCCCATAGCGTGCTCAAAATAGAAACAGGGAAACAATTTGTTCAATGTGAATGAACTCTGTTTGATTGATAGTAGATGGGAAGATAAGAAATATAAATCTGATTCAGATTTGCGAACTCCACTCCCTGTGGATAATAAAGCGAAGTGCAATTCCAGATCTAGAGTATCACTCAGTGTGTAAACTTCACCCTGGCCATAATCACCATGGTCTCACCAGCATCTTCTATGCTTGTTGAATATTTACTGTGAACCAAGCACTTGCCACAGAACGAAAGCTCCATTTCCCAGCCCCAACACAGCCGAAGGCGCTCTGAAATGTCAGCTGGGGGAAAACCAAAGCTTACCTGAGCAAGCGGAAGGTAAGCGGTACAAATGGGATGAGCTCAGGTGGGCATGAGAGCGAAACTCGTGTCTCCGGTTCATGATCCATTGCTTCTCCACCTTACTCTACCTCTAAACACGTCTTTGGAGCTCTTCAGCCAAGATAACTACATACATCTCCAGCCTTGTGCAGGAGTGCCTGGTGGTTCTTTCATTGATGTACGCCCATGTCATCTCTCCTTCTAGGTTCTTGCTTTGCACTACAGAGATGATCTTGTTCTTATACACTAATGTCACCTCCCATCCCAATACATGCCACGTAGCTATCTGCAGTGAAACATAAGCACAGAGTTTACTACTCCCCTGGAGATGCTAATGGCCTAGAGATTGTGCCACATAGCCAAAGATGCCTAAGAGTGATGTGCCAACTCTTTCTGAACCCTGAAAATAAGATCCATCCATCTCATGAACCAAACCAGAAGGCCCAACTGAAGAACCGGTTGCCTAACCATGCTTTTTCTCTTTTGCAG
Seq C2 exon
AATCAGAAATATTTCAAAAGAATACAAAGGAAAGCCCAATAAAATAGAAGCCTTAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020620-Abca8b:NM_013851:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.101 A=NA C2=0.192
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0000522=ABC_tran=PU(1.4=9.5)
Main Inclusion Isoform:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGAATACGGACATCAGCACTCT
R:
AGGCTTCTATTTTATTGGGCTTTCCT
Band lengths:
222-2030
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: