DreINT0023538 @ danRer10
Intron Retention
Gene
ENSDARG00000074635 | abca1a
Description
ATP-binding cassette, sub-family A (ABC1), member 1A [Source:ZFIN;Acc:ZDB-GENE-031006-12]
Coordinates
chr1:51982816-51983146:+
Coord C1 exon
chr1:51982816-51982878
Coord A exon
chr1:51982879-51983039
Coord C2 exon
chr1:51983040-51983146
Length
161 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
GCATTATGTCCCTTCATCAGTGT
3' ss Score
6.17
Exon sequences
Seq C1 exon
GTGTATAAGAGGAAGCAGAAGCCAGCTGTAGACAGACTGTGTGTGGGAATCCCACCTGGAGAG
Seq A exon
GTGAGCTCATCTATCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATATATATATATATATATATATATATTTCAAATTAGTTGGAGTGTACAATTATAATAAGCAAATGGAGAGTTTAATGGCATTATGTCCCTTCATCAG
Seq C2 exon
TGTTTTGGGTTGCTGGGTGTGAATGGAGCCGGAAAGACGAGCACCTTCAAGATGCTAACCGGAGACTCTGTGGTCACCAGCGGAGAGGCCTACTTAGCAGGAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000074635:ENSDART00000142465:42
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=0.000
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=PU(7.6=52.4)
A:
NA
C2:
PF0000522=ABC_tran=FE(24.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTATAAGAGGAAGCAGAAGCCA
R:
CTGTTTCCTGCTAAGTAGGCCT
Band lengths:
170-331
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]