DreINT0023534 @ danRer10
Intron Retention
Gene
ENSDARG00000074635 | abca1a
Description
ATP-binding cassette, sub-family A (ABC1), member 1A [Source:ZFIN;Acc:ZDB-GENE-031006-12]
Coordinates
chr1:51981054-51981721:+
Coord C1 exon
chr1:51981054-51981177
Coord A exon
chr1:51981178-51981591
Coord C2 exon
chr1:51981592-51981721
Length
414 bp
Sequences
Splice sites
5' ss Seq
TCGGTGCGT
5' ss Score
8.67
3' ss Seq
TGTTTTCTGAATGTTTTCAGGAG
3' ss Score
8
Exon sequences
Seq C1 exon
GAGATCGGCGGCATCAATGACATCTTGAAGAACGTGTTTCTGATCTTCCCTCATTTCTGTCTGGGTCGAGGACTCATTGATATGGTGAAGAACCAAGCTATGGCTGACGCGCTGGAGCGATTCG
Seq A exon
GTGCGTGTCTTTTTTTTCTCACGTAAAAAAAGTACTGAAAGTTATCGACAGAAGTAGATCAAAAATATTACTCATGATTATCCGCGTCTGTATTTAAGTGTCTATTGTGACTATATTGTATAAAATATTTGTTTGTAATTCCTGTAATCATACAATAAATCCAAAATAATACATACATTTAAAAATGTTTTCAGAGCATGTGACATTTTAACCACGCAGAAGTACTTCAGACTAATTAAACTTAGCATTTAGGTTTTTTCAATTGTTATTTATGGGTGGAGGGCGGGGCTTGGAGGCTAGAATTGATTAGATGTGAATGGCAGATTGATCCCGCCCTCAAATCTGTGAGCACCAATCAGAGAGGACATGAGAGTATCAGCTTCCGCTGATGTGCTGTTTTCTGAATGTTTTCAG
Seq C2 exon
GAGAGAATCGTTTCCGCTCTCCTCTGGCGTGGGACATGGTGGGCAAGAATCTGTTCGCTATGGCCATCGAGGGCGTGATTTTCTTCAGCATCACCGTCCTCATCCAGTACCGCTTCTGCATTAAGGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000074635:ENSDART00000142465:39
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(11.4=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=PD(9.2=75.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGATCGGCGGCATCAATGAC
R:
CTGGCCTTAATGCAGAAGCGG
Band lengths:
254-668
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]