MmuINT0007925 @ mm9
Intron Retention
Gene
ENSMUSG00000018800 | Abca5
Description
ATP-binding cassette, sub-family A (ABC1), member 5 [Source:MGI Symbol;Acc:MGI:2386607]
Coordinates
chr11:110159350-110161324:-
Coord C1 exon
chr11:110161205-110161324
Coord A exon
chr11:110159552-110161204
Coord C2 exon
chr11:110159350-110159551
Length
1653 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
TGTTACTTTTTGGTGAAAAGACT
3' ss Score
1.34
Exon sequences
Seq C1 exon
GCTTGTTTTCTGCTCTAGACATTCATTCAAACCTGGGTGTTATTTCTTATGGTGTTTCCATGACAACATTGGAAGATGTATTCTTAAAGCTAGAAGTTGAAGCAGAAATTGACCAAGCAG
Seq A exon
GTAAAAACAAAACTAAAAAGATCAGTCAATGAACTGGACAATACAAATAATTATATAAGTAAATGAATTAATTATGTAAGCATATGAAGTCTGCGTTGCCTTGTGGAGCCAAGGGCAGAAGTAAACAAGTAATTGAAATATTGCTAATGGTGAGAAGAGATTATGGAGGAAATGACCTGATATTCTTGGCAAGTCTTATTGTTAGAGAGGGCTTTATTGAGCTGCTTGAAATGAGATGTGAATCCCCAGAAAAATTCACATATGCAAACATCTTAGGGCAAAATGTACTGGATAAAGAAAGTTTCCACTTCTCAGGTGTTATGACATTAATTAGATGTCTTTGAGGGACAAAAAGCAGGCCACCGTGGTGGGAACCATGAAGGAAATATTAGGTGTCGCTATCAGAGAGTAGCCAGAGGGCTGGGTCACAGTTTGCCTTTGATTTTTGTTGTTTTGTTTTGTTTTTTCGAGACAGGGTTTTTCTGTGTAGTCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCTGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGTGTGCGCCACCATGCCTGGCAGGTTTTGCCTTTGAACATCTGGGAAGAGCTTTCTTTAATTTTGAATGCAGTGTCAAAGGGTTTAAAGCAAAAGAATAACTCAGTAATTCTTGGTATGTGTTTTTAGTGAACACACTCGTGTTTGGGAAGGTAGTTCCACAATAGAGTACTTGTCTGGCATCTGCAAGACTTTGGGTTCATGTCTAACACTGAAAAGCATTTCTAATTATTGGATGATAGCTGTAGTGTGAAGGAAGAGCAGAAGATCAGTCAGGAAAACTTGTGTATAAAATTGGGCTTGAATAGGGTGGCAGGAAAACACGCACAGGGTGGATTTGTAGTGTGCTGATCTCAGCAATAATGGTTTGCTGAGGCTTCTTAGGGAGGGATCAAGAGTCATTGTCAAGTTTGGGAACTGCATGTAGTTGCCTCTTCCTGAGAGCAGAGGGGTAGATGCAGAAAGGTAGGACGCATGTTTGCCTTCACTATCTAAGGTTCATCAGAAACTCCATGAGGTGTAAGGGCTGGAGCTGGAAATCTTGAAGTCACGAAGATGCTGTTATGGAGACTGGGGAGAGCCCTTGAATGGGGACAACAGTCAGTGGAAGGGGCACCCTGACGGGAGCAGCTGGGAGAAAAGAAGGGCTGGCATTGTGAGTTTTTCTTCACAAATGAACAGAGAAGCAAAATTTTAGAAAAAGCTGTCTTTGGTGCAAGAGAAAGTGGACTCTTGATTGTCAAATATACAGAGTAAAGCAAGGAAAGAAATCATTCGGAAACAGGATGGTGAGCAGCTTCGTAGGGAGGGAGAAAGTGATGCCCTTGCCAAGAGCATCTTGGGTGGTGTGGCCAAGAGCGCAGGGGAGCTGTGTAGTGCACGGTGAGACAGTGAGCTGGGGATTTCATGACTGAAGCTTAGCATGAGGTCAGTGTGAGAAGATGATGCCAAAGAGTACGTTTCTGTTCCACACCACTTGCAGACATGTGCTGTCATGTTGATGGTTTAGTTGTTGATCTTTCTATTTCAAACATTCCAAAATGGTTTTGTGTTTGTTACTTTTTGGTGAAAAG
Seq C2 exon
ACTATAGTGTATTTACACAGCAGCCGCGGGAGGAAGAAACAGATTCAAAATCCTTTGATGAAATGGAACAGAGTTTACTTATTCTCTCTGAAACGAAAGCTTCTTCAGTGAGCACCATGAGCCTCTGGAAGCAGCAAGTGTCTACGATTGCAAAGTTTCATTTCCTCTCATTGAAACGAGAAAGCAAATCAGTGCGCGCTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000018800-Abca5:NM_147219:18
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=0.074
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF126982=ABC2_membrane_3=PU(1.4=7.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTTGTTTTCTGCTCTAGACATTCA
R:
CGCGCACTGATTTGCTTTCTC
Band lengths:
318-1971
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: