DreINT0023603 @ danRer10
Intron Retention
Gene
ENSDARG00000013500 | abca2
Description
ATP-binding cassette, sub-family A (ABC1), member 2 [Source:ZFIN;Acc:ZDB-GENE-050517-1]
Coordinates
chr5:24621926-24622496:-
Coord C1 exon
chr5:24622316-24622496
Coord A exon
chr5:24622139-24622315
Coord C2 exon
chr5:24621926-24622138
Length
177 bp
Sequences
Splice sites
5' ss Seq
TATGTGAGT
5' ss Score
5.56
3' ss Seq
ATCCAGTGAATATCCCACAGGTC
3' ss Score
4.86
Exon sequences
Seq C1 exon
AGGAAACCCGTGGAATTGAAGAAGAGCCCAATCATTTGCCGCTGGTGGTGTGCATCGACAAACTGACCAAAGTCTACAAGACGGGCAGCAAACTGGCTCTAAACAAGCTGAGCCTGAACCTGCATGAGAACCAGGTTGTCTCTTTCTTGGGACACAATGGGGCTGGCAAGACCACCACTAT
Seq A exon
GTGAGTGTTAGGTCATTGTGTTTCATTGTGTATGAGGGTGATTCATACCCTCTGGACCCATGCTGTGCTTGTTATTGGGACTAACAATGGCATCCTATAACCTGAAAATTGGATGTCCACATAAAACTGATGTTTCTTGCGGAATACTGTATTCATCATCCAGTGAATATCCCACAG
Seq C2 exon
GTCCATTCTCACGGGACTCTTTCCACCCACCTCTGGCTCTGCCACCATATACGGCCATGACATCCGCACAGAGATGGAGCGCATCAGGCAGAACTTGGGCATGTGTCCCCAGCACAACGTCCTGTTTGATAAGCTCAGTGTGGAGGAACATCTGTGGTTCTACTCACGGCTGAAAGGCATGGCAGAGGAAGATATTCGCAAGGAGATGGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000013500:ENSDART00000141554:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.115 A=NA C2=0.042
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=PU(18.6=44.3)
A:
NA
C2:
PF0000522=ABC_tran=FE(49.0=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:
CTGAGCCTGAACCTGCATGAG
R:
TCAGCCGTGAGTAGAACCACA
Band lengths:
247-424
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]