DreINT0023506 @ danRer10
Intron Retention
Gene
ENSDARG00000074635 | abca1a
Description
ATP-binding cassette, sub-family A (ABC1), member 1A [Source:ZFIN;Acc:ZDB-GENE-031006-12]
Coordinates
chr1:51964298-51964975:+
Coord C1 exon
chr1:51964298-51964474
Coord A exon
chr1:51964475-51964752
Coord C2 exon
chr1:51964753-51964975
Length
278 bp
Sequences
Splice sites
5' ss Seq
CATGTAAGA
5' ss Score
5.58
3' ss Seq
TGCTTTCTCCTGTTGTCCAGTTT
3' ss Score
5.98
Exon sequences
Seq C1 exon
ATATTGGGATCCGGGTCCTCGAGCTGACCCATTTGAGGACTTGCGTTACATCTGGGGCGGCTTCACATACCTGCAGGACGTGATTGAGCACGGGATCATCAGAGCTCTGACCGGCAGCAAGGAAAAAACCGGAGTCTACATCCAGCAGATGCCGTATCCCTGCTATGTGGATGACAT
Seq A exon
GTAAGAGAGATCATCACCATTTACAGCCTTTATATTCATATGCAGATTTCAGTCACAATTAGAACAGAGTGACATGTAAGCCCTGTTATTGAAATACAGTGGCATATAAGCTTTGTTTTTTTAAATATAGTGATCTATATGCTTTGTTTTTGAAAAATAGTTGTAAATATATAAGCTCTATGTTTTAAAAATAAAAAAACAGTACTCCTGCATGTTTTAATAAAAATAAATCAGCCATTTTAGTGATTGTGTGACCCCTGCTTTCTCCTGTTGTCCAG
Seq C2 exon
TTTCCTGCGGGTCATGAGCCGCTCCATGCCTCTCTTCATGACTCTGGCCTGGATGTACTCGGTGGCCATCATCATCAAGGGTGTGGTGTATGAAAAAGAGGCCCGACTCAAGGAGACCATGCGGATCATGGGTCTGGATAACGGCATCTTGTGGCTGAGCTGGTTCATCAGCAGCCTGATACCACTGCTCATCAGCGCCGCCCTGCTGGTGCTCATCCTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000074635:ENSDART00000142465:13
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(16.6=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(20.8=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:
GGACTTGCGTTACATCTGGGG
R:
GCCACAAGATGCCGTTATCCA
Band lengths:
296-574
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]