DreINT0023509 @ danRer10
Intron Retention
Gene
ENSDARG00000074635 | abca1a
Description
ATP-binding cassette, sub-family A (ABC1), member 1A [Source:ZFIN;Acc:ZDB-GENE-031006-12]
Coordinates
chr1:51966617-51967026:+
Coord C1 exon
chr1:51966617-51966821
Coord A exon
chr1:51966822-51966912
Coord C2 exon
chr1:51966913-51967026
Length
91 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGA
5' ss Score
7.41
3' ss Seq
TAAAAAAATCTCTCTTACAGGTC
3' ss Score
10.64
Exon sequences
Seq C1 exon
AGTCTGCTGTCTCCAGTGGCGTTCGGCTTCGGCTGTGAGTATTTCGCTCTGTTTGAGGAGCAGGGTGTGGGCATCCAGTGGAGTAATCTGCTGTCCAGCCCCATGCAGGAGGACAGCTACAACCTGACCACCTCCATCTGCCTCATGCTCTTCGATTCGGTGCTCTACGCCGTCATGACCTGGTACATCGAGGCCGTCTTTCCAG
Seq A exon
GTCAGAATCTGGCTTTTCTGAAGCTGCTTGTCATGTGTGATAATTATTAGACTGGGTAAATGATACAGGTGTAAAAAAATCTCTCTTACAG
Seq C2 exon
GTCAGTATGGCATCCCTCGACCCTGGTACTTCCCTTTCACCAAGTCATACTGGTGCGGAGAGAAATGCGGATGGACAACATCAGTGCCAAGTAACAGGAAAGAAAACGCGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000074635:ENSDART00000142465:16
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=0.026
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=PD(17.2=88.4)
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:
TGTGGGCATCCAGTGGAGTAA
R:
AAGTACCAGGGTCGAGGGATG
Band lengths:
171-262
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]