MmuINT0008142 @ mm10
Intron Retention
Gene
ENSMUSG00000041797 | Abca9
Description
ATP-binding cassette, sub-family A (ABC1), member 9 [Source:MGI Symbol;Acc:MGI:2386796]
Coordinates
chr11:110100749-110102566:-
Coord C1 exon
chr11:110102511-110102566
Coord A exon
chr11:110102064-110102510
Coord C2 exon
chr11:110100749-110102063
Length
447 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
TTATGCGTTCTCTTTTCCAGGTC
3' ss Score
13.75
Exon sequences
Seq C1 exon
TGAAAGAGAATTTTGACCTGGAAGAATACAGCCTCTCACAGTCTACTCTGGAGCAG
Seq A exon
GTGGGTAACTTTTAGTGATTATATATAATCCTAAAAAGTTTAGAGCTGGAAAGATGGATCAGCAGATAAAGCTCTTTCTGAACAAGTGTCAGGACTATAGTTTGAACCTCTAGAATCCGTATAAAGCCAACTCAACATAGCTGACTCCTGTAGCCCTACCATCACAGAAGCATCTGGCTAGCAGGATTAGCTAAGTGGAGAGCTCTAACTTCACATAGAGAAATCGAAAAGGCTACCTGAGATCAACTCCAGGCATTCACGGATACCAGCATGTAATGGACCAATGCACATGTGGCCATAAATTACACACATGCATATACATGCAAAAGAGAAGATCAAGTAAGCCTAGGAAGTATATAACCTTTGCATCGTTTGCAGCTACAGGAGGTAGCGTGGCATGCCTCTCGTTCTTTTTTTTCGTTTTTCTTTATGCGTTCTCTTTTCCAG
Seq C2 exon
GTCTTCCTGGAGCTCTCCAAGGAGCAGGAGCTGGACGACTTTGGCGAAGAAGCCAATTCCTCAGTGAAATGGAAGCTCCTCCCACAGGAAGAGCTGTAAAGTTCAAAGTCCTCTCTGTATCCTCAAGCTCACATCCCTCTTACAGACAGTATATTTAAGAGCATCACTGTGCCTTACTTGGTCGGTGTGCAAACAGCTTAGAACACGCAGCCAGACTACGCTCAATCAAGTCACGTTGCACACAGTGTGGAGTTTTAAACTGCATTTACAATAGTATTGATGCTTCTGAGCATGCTAAAGAGACTGATTGATTTTCTTCGCCTGAACTTCAAAACATTAACTTTTTTCTTTCCTCCGTGTCTAGGTAAGGTATAATGTAAACAATATTGATTTTAGGGAGAAGAGGATCAATTGATTTCCCAACAGCACAGTATTTGTTTTTTTGTGTAACTCACCCTGACCTGTCTGTCATTCACTAGTTCTTTACTCACAGTTTGCCCACTCTGAGTTACGGAGAAATGTTTTGTCCACTGTGACTGACTGCGGAAGCAACTTTAAACTGGTGGACGTAAATACTTGCAACCATTAAATAACTGTGTGCATGTTTACATACGAATCTGAAACATTTCTGAAATTTTGATTTGGGAAAAAGTAATGCAGAGGAGGGGTACTCTTAGGTCCAAGGACTGGCTTTGTATGTATTTATTTACCAAGTCTGTGAATGCTACAACCTCTCTACTGCAACATCAGTACAGTTACCTGGACTCTTATCTAGGAGATTTTTTTGTTGTTACTACTAGTATTGTTACTAATTAACCAAACATCTATATGAAATTATAAGTTAATATGAAAAAATTATATGAAAAAAAATTCCCTTGATGCTAAGATTGTAACTTCATAGTGTATGTGAATATCAACTGCCCTCAACTTACAAGGAGACTTCTCAAGTAGACTTTGAGCAAAGGCTCTAAGCCTTTAAAGTTAAAAAGAGACATTAATGCTGGACTTGCTGATGTACCTGCTTTATGAATAACAACTTAATCCGTACACATCAATGCATTAAAAACACTTTATTTAGGGTCAGAAAACTGCCTCAGCTGGTTAAGGTGCCCAGTTGTCAAGTCTGATGTCCAGAGTTTGATCCTTGGGTGGGACCCAAATTGTGGAAGGAGAGAACCATCACTCAAGCTGTTTTCTGATCTCCACATACATGTAGTGTCAGGCGTATATGTCTACATACCTGCACTCAGGACAAACAAACAAACAAACAAAATTTAAATAAAAATATAATGGGCTTTCCTGTGGTGTTTTCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041797:ENSMUST00000044850:38
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
AGCCTCTCACAGTCTACTCTGG
R:
TGAAGTTCAGGCGAAGAAAATCA
Band lengths:
358-805
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