MmuINT0008136 @ mm10
Intron Retention
Gene
ENSMUSG00000041797 | Abca9
Description
ATP-binding cassette, sub-family A (ABC1), member 9 [Source:MGI Symbol;Acc:MGI:2386796]
Coordinates
chr11:110108821-110110447:-
Coord C1 exon
chr11:110110287-110110447
Coord A exon
chr11:110108897-110110286
Coord C2 exon
chr11:110108821-110108896
Length
1390 bp
Sequences
Splice sites
5' ss Seq
ACGGTATGT
5' ss Score
9.94
3' ss Seq
CCACTCATTGTGTTTCTCAGGTT
3' ss Score
9.05
Exon sequences
Seq C1 exon
GTGTTTTTGAAAGGGAGCGGTGGGGGTGCTGCCCTCGGATTCTTGGGGTACTGCCCTCAGGAGAACGTGCTGTGGCCCAACCTGACAGTGAAGGAACACCTGGAGTTGTATGCTGCTGTGAAGGGGCTGAAGAAAAAGGATGCTGTGGTCACCATCACACG
Seq A exon
GTATGTGGAGAAGCCGCACTTAATCCCTGCTCAGGACAGTGGTATCTTATTAATGTGCTCACACAGAATTAAAGAAGAGAGCTTCTAACTACTGTTCCCTTGCTTGTGGGACACTTAGTCATCCCGAATGGGTTCACTGCTGTTCTCTCTTACTTTAAGCCTGGAGAGAAAGGTTTACTGATCTTTCCTTCGTTCCTTCCTTCGTTCCTTCCTTCTTTCTTTCTTTCCTTCCTTTCTTTCCTTCCTTCCTTCCTTTCTTTCTTTCTCGCTCTCCCTCCCTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTTCTTTCTTTCTTTCTTTCTCTCTCTCTCTCTGTCCCTCTCTCTCTCTCTCCCTCCCTCCCTCCCTCCCTCCCTTCTTTCTCTCTCTCTCTCTCCCTCCCTCCCTCCCTCTTTCCCTTCCTTCCTTCCTTCCTTTTATTCTTTTTTAGAAGAAAATATCTATTGGGCTTATTACCAGAAAGACCAGTCCATTGTGGTGGGGAAACATGGAAAATAATAGTGGAAATAAGAGTGTGTTGACCAAAGAGAGCTATAAAATATCAGTATTAGCCAGTTTTGTGTTATTGTAATGAAACTCAGTAGTCTGAATACATTTGAAGAAAAGAGATTTATTTATTGAACCCACTTTATATTTGTTTTGTTTTTGTTGTTGTTGTTGTTATTGTTACTGTTTTTGAGACAGGATTTCTCTGTGAATCCTTGGCTGTCCTGGAATTCACACTGTAGAACAAGCTGGCCTTTGACTCACAAAGATCTGCCTGACTCTGTTTACCAGTGCTTGTATTAAAAGCTTGTGCCACAACCACTGTCCTGCTATTTAATTCAGTTTTGAAGACGAAAGTTCAAGATGTCAGCTTTTGCTTTAGCCTCTAATGAAGGCCAAAGAACAACGGTATCAGTGCAGGGTTGTGTGTGAGTGAGAGAGATGATATGACCAGACAAAAAGCCAGAGAAATGAGGACTGTATAATCCAAGCCATAGCCTTGTGGATCTAGAGTGGTGGTTCTCATCCTTCCTAATACAAGTTCATCATGTCGTGGGGACCTCCCAACCATAAAATTATTTTGTTGCTACTTCATAACTGTAATTTTGCTGCTGTTATGAATAGCAATGTAAATATATGGTATGCAGAATATCTACTGTCTAAACAGTAGCAGGAACCTAAGGACTGTCAAAAGTGTGACCTCTCTGATGACTTTAAAAGCTCTCACAACCATAATATTGTGCAGATATGTTTGCTACACTCCCTCGTGTTCCTGCATAATGAAGATCCACTCATTGTGTTTCTCAG
Seq C2 exon
GTTGGTGAATGCCCTTAAACTGCAGGACCACTTGAAGGCTCTTGTCAGGACCTTGTCAGAGGGAGTGAAGAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041797:ENSMUST00000044850:32
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=0.000
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=FE(37.6=100)
A:
NA
C2:
PF0000522=ABC_tran=FE(17.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTTTTGAAAGGGAGCGGTGG
R:
TCTTCACTCCCTCTGACAAGGT
Band lengths:
230-1620
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