DreINT0023536 @ danRer10
Intron Retention
Gene
ENSDARG00000074635 | abca1a
Description
ATP-binding cassette, sub-family A (ABC1), member 1A [Source:ZFIN;Acc:ZDB-GENE-031006-12]
Coordinates
chr1:51981592-51982045:+
Coord C1 exon
chr1:51981592-51981721
Coord A exon
chr1:51981722-51981924
Coord C2 exon
chr1:51981925-51982045
Length
203 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TTCTGTGTTGGTGTTTATAGGTC
3' ss Score
9.26
Exon sequences
Seq C1 exon
GAGAGAATCGTTTCCGCTCTCCTCTGGCGTGGGACATGGTGGGCAAGAATCTGTTCGCTATGGCCATCGAGGGCGTGATTTTCTTCAGCATCACCGTCCTCATCCAGTACCGCTTCTGCATTAAGGCCAG
Seq A exon
GTGAGGATACTTTTGTCAATACATTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTGTGTGTGTGTGTGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGATTATTTTGAAATGCATGTGATTTAATTTTTATACAATCTTCTGTGTTGGTGTTTATAG
Seq C2 exon
GTCACTTAGCACTAAGCTGAAGCCAATCGGAGAGGAGGATGAGGACGTAGCCCGAGAGAGGCAAAGGATTCTGGGAGGAGGAGGACAGACTGATATCCTGGAGCTCAGGCAGCTCACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000074635:ENSDART00000142465:40
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=0.049
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=PD(9.2=75.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATCGTTTCCGCTCTCCTCTG
R:
CTTGGTGAGCTGCCTGAG
Band lengths:
246-449
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]