DreINT0023619 @ danRer10
Intron Retention
Gene
ENSDARG00000013500 | abca2
Description
ATP-binding cassette, sub-family A (ABC1), member 2 [Source:ZFIN;Acc:ZDB-GENE-050517-1]
Coordinates
chr5:24603371-24603756:-
Coord C1 exon
chr5:24603582-24603756
Coord A exon
chr5:24603487-24603581
Coord C2 exon
chr5:24603371-24603486
Length
95 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGT
5' ss Score
8.35
3' ss Seq
TTGTCCTTCCGCCCCTTTAGCTG
3' ss Score
8.64
Exon sequences
Seq C1 exon
GCTCCAGGGCACTGATGTGGTTATTGCCATCTTCATCATTGTAGCCATGTCTTTCGTGCCTGCGAGCTTTGTGGTCTTTCTGGTAGCGGAAAAATCCACCAAAGCCAAACACCTGCAGTTTGTCAGCGGATGCGACCCTGTCACGTACTGGCTAGCAAACTACATATGGGACATG
Seq A exon
GTATGTTGAAGGAGAGACTGACTGTGTGTGTAAAACTTTCCTGAGGGCTTAACTAGTTTACACACAGATTTGTTTTTGTCCTTCCGCCCCTTTAG
Seq C2 exon
CTGAACTACCTGGTTCCAGCTACATGCTGTGTCCTAATTTTGTTTGTGTTCGACCTTCCTGCGTACACGTCACCTACAAATTTCCCAGCAGTGCTCTCTCTGTTTCTGCTTTATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000013500:ENSDART00000141554:33
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:
PF126982=ABC2_membrane_3=FE(18.7=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(12.3=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:
TGTGGTCTTTCTGGTAGCGGA
R:
TAGGTGACGTGTACGCAGGAA
Band lengths:
182-277
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]