DreINT0023514 @ danRer10
Intron Retention
Gene
ENSDARG00000074635 | abca1a
Description
ATP-binding cassette, sub-family A (ABC1), member 1A [Source:ZFIN;Acc:ZDB-GENE-031006-12]
Coordinates
chr1:51969077-51970152:+
Coord C1 exon
chr1:51969077-51969216
Coord A exon
chr1:51969217-51970014
Coord C2 exon
chr1:51970015-51970152
Length
798 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
AAAAAGATCTAACCTTGCAGGAG
3' ss Score
4.75
Exon sequences
Seq C1 exon
GCTGACCGTGGAGGAGCACATCTGGTTTTATGCGCGTCTGAAGGGTTTGTCTGCGGAGAAGGTGAAGTCTGAGATGGAGCAGATCGTGATGGACCTCGGCCTTCCTCATAAACGCACATCTCGCTCCAACCAGCTCTCAG
Seq A exon
GTATGGAGATTATATAAAAACACAAAGAGATCTTGCTCTACAATTTATACGATTTCACCAAGGATGCATTTATTTCATCAACAATACAGTAAAAACTGTAATATTATTAGGATTTCAATGAACTTTATTTTCTGTTTGGATATATAGTTTTCATTTAAATTCATTCCTAAGGTTAAAAGCTGAATTTTCAGCATCATTGCTGCAATTTTTAGTGTCCCATAATCCTTCAGAATCTATTGAAATATTTTTAAAATGTTGAAAACTTTTCAGATTTTGCTGAAAATCTATGATTTTTTTTATATAATATAAAGTTTTATAAATCTTTGTAAAATTATAAATGACTTTAATGTCATTTTTATCAATTTAATGCATCCTTGTATTAAAGAATTAAAAATATCTGCATTAATTTTAAAGTATTAGTATTGATCTTACTGATTTGTTTTTCTATTTTTTGCATTGCTAAATTTCCATCAAAAGCTCAAAGTAGCTTTATATGCTTTTCCTTAGTAGTTTAATCACATGTGAAGGTAAAAGATTCTATCAAAATATTTAAAATATCTAACCTTGTAACATAATAAATAATTTACTGTCATTTTCTTATTAATTTAATGCATTCCAGGTGTAAAGAAATAAAAATATTTAATATTTTGGGTATTAGTATTGATCTTGCTGATCATTTTTTCTAGTTTTTGCATTGCTCAATTTCCATCAAATGCTCAGAGTAGCTTTATATGCTTTTCGTAAATAATTTAAGCACATGTGAAATGTCAAATTATTTAAAAAGATCTAACCTTGCAG
Seq C2 exon
GAGGAATGCAGAGGAAGTTATCAGTCGCGCTGGCCTTCGTCGGAGGCTCAAAAGTGGTGATTCTGGATGAACCGACTGCTGGAGTTGATCCTTACGCCCGCCGTGGCATCTGGGACCTGCTGCTGAAATACCGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000074635:ENSDART00000142465:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.104 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=FE(32.4=100)
A:
NA
C2:
PF0000522=ABC_tran=PD(17.9=55.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGACCGTGGAGGAGCA
R:
CTTGGCGGTATTTCAGCAGCA
Band lengths:
278-1076
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]