DreINT0023627 @ danRer10
Intron Retention
Gene
ENSDARG00000013500 | abca2
Description
ATP-binding cassette, sub-family A (ABC1), member 2 [Source:ZFIN;Acc:ZDB-GENE-050517-1]
Coordinates
chr5:24596258-24596751:-
Coord C1 exon
chr5:24596610-24596751
Coord A exon
chr5:24596393-24596609
Coord C2 exon
chr5:24596258-24596392
Length
217 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGC
5' ss Score
8.19
3' ss Seq
TCTCTATTTGTGTCCTGAAGGTG
3' ss Score
8
Exon sequences
Seq C1 exon
TATCTTGCGGGAGCTGTTACGTGTGCAGCAGAGCATCGGTTACTGCCCTCAGTTTGACGCTCTGTTTGATGATCTGACGGCTCGAGAGCATCTGGAGCTCTACACGCGCCTCCGCGGCATCCCATGGAAAGATGAGGAGCGG
Seq A exon
GTGAGCACACAGACACGCATGCTGAGCAGTGACAGAGCATTCTGTTCATGCGCTTATCAGTGATCATTGAGGGAGGATAAGAGCTTATGGAGGCTCTCCTGAAATCAGCTCGAAGAGTGTGACCATCTATAATTAGAAACTGCAAAATTAATTGTTCATAGTGCGAGAAATAGCAAGTGTTTATTTTTTGCTTTCTCTCTCTATTTGTGTCCTGAAG
Seq C2 exon
GTGGTTCAGTGGGCTTTGGAGAAGTTGGAGTTGTCCAAGTATGCCGACAAGCCTGCTGGCACCTACAGCGGAGGCAACAAACGCAAACTCTCTACAGCCATTGCTCTGATTGGATACCCATCGCTCATCTTTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000013500:ENSDART00000141554:40
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=0.000
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=FE(32.4=100)
A:
NA
C2:
PF0000522=ABC_tran=FE(30.3=100)
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:
GGGAGCTGTTACGTGTGCAG
R:
CAAAAAGATGAGCGATGGGTATCC
Band lengths:
269-486
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]