DreINT0023515 @ danRer10
Intron Retention
Gene
ENSDARG00000074635 | abca1a
Description
ATP-binding cassette, sub-family A (ABC1), member 1A [Source:ZFIN;Acc:ZDB-GENE-031006-12]
Coordinates
chr1:51970015-51971303:+
Coord C1 exon
chr1:51970015-51970152
Coord A exon
chr1:51970153-51971070
Coord C2 exon
chr1:51971071-51971303
Length
918 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAC
5' ss Score
8.14
3' ss Seq
AGAACATGGTTTGTTTTCAGGTC
3' ss Score
8
Exon sequences
Seq C1 exon
GAGGAATGCAGAGGAAGTTATCAGTCGCGCTGGCCTTCGTCGGAGGCTCAAAAGTGGTGATTCTGGATGAACCGACTGCTGGAGTTGATCCTTACGCCCGCCGTGGCATCTGGGACCTGCTGCTGAAATACCGCCAAG
Seq A exon
GTAAACATCTGCAATAAAAAACAGCCTTTAATTACAATAAATATGTCATGCAAAAAAAAATGTTATCCAAGTGCACATACAGTAAGATAAATACAATAAATGTCATATAAACCAAATAAATTAAGGCATTGCTTGTAACAGATCTGCTTATAACAAAACCATCATCATGTAATGCACTTTAAAAGATGCACCAAGATGTCTCTGATGTCCCCAGAGTGTTTTTGTGAAGTTTCAGCTCAAAATACCACACATAATGTTTTAAAACTCTTTTAAGGCTCTCTTTTAGGCTTTGATCCTAATTCTGCTTTAAATTCAAATGAGATTGTGCTCTTTTCAGAAGAGGGCGGAGCTACAAATGCCTGTGTGTCAGCATAGTGGCAGATTCAAAAACCAGACTAATGTTATATGCTAATGAGGGAGCATATCTGACAACATTCAGATCATAAAATCCGGGAGATTTTATCCGGGGCTGTGCGTGAAGTGAATAGCGGGGTGGGGGGGGTTGTTGGTGCACGAAATGAAGAGTGGGGGGTGAGGGTGGGGTTGGGGGGTGGAATTCCGGGAGTTTTGTGTGAGACAGAACAATATGGGAGATGGCCGGGAGATGGGTCTGAAATACTGGAGACTCCCGGGAAAAACGGGAGTGTTGGCAGGTATGTGAGGGAGAGATGGTGACTAATGGGCGGGACTTTCCCCCTCTGATTGACACATACAACGGCAGAATGTCAATCAAAGTGTTTCTGCAGAAAAAATGCAATTAATACATTTCCACCATTAAAAGCTGCTTATATTCACAGATTGTTGCCACTCGACTGTGTTTAAACCCCTTATAAAAGGGATTTTTTGCATAATATGACCCCTTTAATAACTATTCAATCAACTGGTGCTTCTAGTATTAAGAACATGGTTTGTTTTCAG
Seq C2 exon
GTCGCACCATCATCCTGTCCACACACCACATGGATGAAGCCGATATACTGGGCGACCGCATCGCCATCATCTCTCATGGCAAGCTGTGCTGCGTGGGCTCCTCTCTGTTCCTCAAGACTCAGCTGGGCACGGGTTACTACCTGACGCTGGTCAAGAAAGACTTCGATCTGTCCGCCAGCTCCTGCCGCACCTCCAGCAGCACGGTCTCCTACTCCAAGGGAAGCCTCAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000074635:ENSDART00000142465:21
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=PD(17.9=55.3)
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:
GGAAGTTATCAGTCGCGCTGG
R:
TGAGGCTTCCCTTGGAGTAGG
Band lengths:
354-1272
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]