DreINT0023548 @ danRer10
Intron Retention
Gene
ENSDARG00000074635 | abca1a
Description
ATP-binding cassette, sub-family A (ABC1), member 1A [Source:ZFIN;Acc:ZDB-GENE-031006-12]
Coordinates
chr1:51957212-51958057:+
Coord C1 exon
chr1:51957212-51957455
Coord A exon
chr1:51957456-51957917
Coord C2 exon
chr1:51957918-51958057
Length
462 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
ATCTGTCTCTTTATTCTAAGCGC
3' ss Score
6.61
Exon sequences
Seq C1 exon
TTGGCGAGTATGAAGAGCTGGCGCGACATGCGGAATGAGATCCTCTACCTGACGGGCAACAGCACGCAGTCACCAAACCACATGTACCAGGCCGTGTCCCGCATCGTCTGCGGCCATCCGGAGGGTGGCGGATTAAAGATCAAGTCCCTCAACTGGTTCGAAGACAATAACTACAAAGCCCTGTTCGGAAACAATGGCAACGACAGTGACAGCGAGCCCGCATCTGTTTACGACAACTCCTCCA
Seq A exon
GTGAGTGACGCCCTGTATTTATCTGCTTCTTTCCTTGCAAATAATTGTGATCGATGTGAACTTCTCATCATATTTATGTCTGTAAATATGTAGTTGTAGTCAGAATTATCAGCCATTCTGTGATTTTTATTATTTATTTATTTAAAAAAAAACGCTGTTAAAAAATCGGATGTGCATCAGTATACTAAATCCGCGCATGCCTTATATTGGTGTGTTCTGGAAAAAAAAAAACTGACTCAAATCAGAAACCTTTTTGCTGTGAGGCAACAGTGCCAACCACTAAGCCACCGTGTCGCCCTCACAACCAACATGATAACTATAAATATAAGATCAATTGTATTTACTGCAGTGTCCATACAGATAAACAAACTAAATAGTTCTGTTTGTCATAAGTGTGATGTGCAGTTTCTTTATGCATTGTGCTAAATGTTTGACTATTTCTATCTGTCTCTTTATTCTAAG
Seq C2 exon
CGCCGTACTGCAACAACCTGATGAAGGGTCTTGAGTCGAGTCCCATTTCCCGCATGATCTGGAGGGCCCTGAAACCGCTGCTCATGGGAAAGATCTTGTACACACCAGACACTCCGGCCACACAGAGGATCATACATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000074635:ENSDART00000142465:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.122 A=NA C2=0.043
Domain overlap (PFAM):
C1:
NO
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:
GAGATCCTCTACCTGACGGGC
R:
GTATGATCCTCTGTGTGGCCG
Band lengths:
343-805
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]