RnoINT0009979 @ rn6
Intron Retention
Gene
ENSRNOG00000018126 | Abca1
Description
ATP binding cassette subfamily A member 1 [Source:RGD Symbol;Acc:631344]
Coordinates
chr5:69869653-69870126:-
Coord C1 exon
chr5:69869997-69870126
Coord A exon
chr5:69869774-69869996
Coord C2 exon
chr5:69869653-69869773
Length
223 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TTTTTCTTACTGTTTCCAAGACC
3' ss Score
6.19
Exon sequences
Seq C1 exon
GGGAGAACCGCTTCGTCTCTCCACTCTCTTGGGACTTAGTAGGACGGAACGAAAATGCCATGGCCGTGGAAGGGGTGGTGTTCTTCCTCGTTACGGTTCTAATCCAGTACCGATTTTTCATCAGGCCCAG
Seq A exon
GTGAGCTTTATCTCAGAACACTTTCAGGAACTTAACGGGTGCAAAGGGGACCCATGAGCCGTGGGTGACTGCGCTGAGCCAAGCTCACCCAGTTAAACTGATTTTCCAGCCCTGAGCATGCGCTGTGCACCCTAGGAATGACCGCAAGTGGGCTTAGCCTTAGAAACTTGAGTTTTGCCTTGGAAAATAGCTAAAAAGGTTGATTTTTCTTACTGTTTCCAAG
Seq C2 exon
ACCTGTAAAGGCGAGGCTTCCTCCTTTGAATGACGAGGACGAGGACGTGAGGAGGGAGAGACAGAGGATTCTGGAGGGTGGAGGACAGAATGACATCCTAGAGATCAAAGAACTGACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018126:ENSRNOT00000024564:42
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=0.293
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=PD(6.3=75.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGAACCGCTTCGTCTCTCCA
R:
TGGTCAGTTCTTTGATCTCTAGGA
Band lengths:
247-470
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]