DreINT0023601 @ danRer10
Intron Retention
Gene
ENSDARG00000013500 | abca2
Description
ATP-binding cassette, sub-family A (ABC1), member 2 [Source:ZFIN;Acc:ZDB-GENE-050517-1]
Coordinates
chr5:24625442-24625895:-
Coord C1 exon
chr5:24625691-24625895
Coord A exon
chr5:24625601-24625690
Coord C2 exon
chr5:24625442-24625600
Length
90 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
GTTTATCTGTTGTCTTCCAGGGA
3' ss Score
10.6
Exon sequences
Seq C1 exon
TCTTTGATGTCTACCACAGCGTTCGGTCTGGGATCCAAGTACTTTGCCCTGTATGAAGTGGCTGGCGTGGGAATTCAGTGGCGCACTATTAACCAGTCACCTGTAGAGGGCGATGACTTCAATCTACTGCTGTCTATGGTCATGCTCACTATTGACGCCATTGTATATGGTGTGTTGACCTGGTATATAGAAGCCGTCCATCCAG
Seq A exon
GTAAGCTGCGGCCCTACAGTCATTATTATGAAGGTAAACTGTGCCTATTTCTTTTCAGTATTTGATTTTGGTTTATCTGTTGTCTTCCAG
Seq C2 exon
GGATGTATGGACTGCCTCGGCCATGGTATTTCCCCTTGCAGAAGTCCTATTGGTTAGGTAGTGGCCGCATAGAGACGTGGGAGTGGCCGTGGGGTGGAGGCACCAGGCTGAGTGTTATGGAAGAGGACCAGGCTTGTGCCATGGAGCATAGACGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000013500:ENSDART00000141554:17
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=0.111
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=PD(13.9=88.4)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGAATTCAGTGGCGCACTAT
R:
TGCAAGGGGAAATACCATGGC
Band lengths:
177-267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]