MmuINT0008131 @ mm10
Intron Retention
Gene
ENSMUSG00000041797 | Abca9
Description
ATP-binding cassette, sub-family A (ABC1), member 9 [Source:MGI Symbol;Acc:MGI:2386796]
Coordinates
chr11:110115444-110117150:-
Coord C1 exon
chr11:110117059-110117150
Coord A exon
chr11:110115565-110117058
Coord C2 exon
chr11:110115444-110115564
Length
1494 bp
Sequences
Splice sites
5' ss Seq
CAGGTTGAC
5' ss Score
1.3
3' ss Seq
ACATGCCATTTTGCCTTTAGAAT
3' ss Score
8.48
Exon sequences
Seq C1 exon
CCTTACCTTCACTTTCTTCTTTTCTTTTTCATTCTGCGATGTCTGGAAAGATACCTCAGGAAGAAGTCACTGAGAGTGGACCCTGTGTTCAG
Seq A exon
GTTGACAGCATTCAAATAGAATTTCATGTTTCATTTAACATTTATTCTCTAGACATTTTAATATGCCTGAATTAATTGGGAGGGGGAGATCAGGGTTGTTTTGAAGGGCTTGTATTGTCGGCAAAATTATTATAATTCAATCTTACAGTCTAGTGAGAAAAGCAACATTAGTGTACATAAGACGTCAAATTAGGAGAGAAGGAATTCTACTGGCACACTTGAGATACAAGAGATAGTATCTTTAAAAGGACAGATAACTACAGATAAGCAACTGGACCCATGTTGACAGTCCAAGAAGGAAATACATGTGAGCAACAAGACAAAGGTTGAGATGCCTGCCCTTTTCCCACAGACTTGTGAAGACAGATGGGGCAAATTTAAAGGCTTATATAGGAAAATAGCAGAAAATAAAAGTAAAGCTGGATATTGGAAGATAATCAATAGGGAAGTATGGGGAAGAGATTGAACATTACTTCATGAGAAACTAATACATAAATGTGTTTGACACACCATCTTAGTTAATCTTCGGTTTCCTTGTAGAGATGCCATTCCTAAAGCAGCACTTAACTGGGTCTTGCTTAATGTTTGAGAGGTTTAGTCCATGATTATCATGATGAGAAGCAGACAGGCCTGGTGTTAGAGCAGTAGCCCAGAGCTTTACATCCTGATGCACAGACGGCAGGCAGAGAGATCGAGGGGGAGACTGGGCCTGGCATGGGCTTTTGAAATCTCAAAGCCCATCCCTTGTGACACACCTACTCCAACATGGCCACACCTAACCCACCAGAACCACACCTACTTCTTAATCCTTCCAAAGCAGTTCCACTATCTGGTGACCAAACACTCAAATACCTTTGACTATGGAGGCCATTTTTTGTTCAAACCACCGCACACACCTTGCTTACCCCACAAGATGAAAACCAAATTCAAATCTAAGTTTGAAGAAAAGAAGAATGACAAGATGACATCATGTTTTATGGAAACCAAGCAAGCATAGTGATTAAGGTTACCCAAGGGAGAGAAGAAACAATCAGCTGACTCAGTTATAGTTGATGAAAGGTCTTGTTTTATAGCAGTGGGAAGGACTGACTGACAGATTTCTAAGGAGTAACATGCCAAGTAACTGAATACACATAGGGATTCTGCTCAGACACCCTGGACTGGTGAGATAGGTTCCTAAATAATGTGCTCTGGCCCTTCATTCTTAGGAAACTTTGGGAATTATAAACCCAAATGCATTTCTAGATCTCTTTTCTTGAGGAAAGCTGCCTTGATATCCACTGACAGAGGATGTGTGCTGCTTTGCTAGTTGAAGAGAGAGAATGGCATCACCTAATTAGGAGACGTAGATCAATGTACAAAGCAAAAGTGAATAGCAGCATCGTTTGACCAGTTGATGGAGAGGGATGAGGGTATTTGAATGGTACACGACAGAGTAGAAGAATGAGTTGTATTTCGATAACTGATAAGCTGAACATGCCATTTTGCCTTTAG
Seq C2 exon
AATTTCTCCGAGAAGTTGTCCTGCTGTTCCGAACCCAGAAGAGCCCGGAGAAGAGGATGAAGATGTTCAGATGGAAAGAGTGAGAACAACGGGCGCCATGGCTACCCTACAGACTGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041797:ENSMUST00000044850:28
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=0.415
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=PD(3.7=35.5)
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:
CCTTACCTTCACTTTCTTCTTTTCT
R:
AGTCTGTAGGGTAGCCATGGC
Band lengths:
207-1701
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