DreINT0023641 @ danRer10
Intron Retention
Gene
ENSDARG00000100524 | abca3b
Description
ATP-binding cassette, sub-family A (ABC1), member 3b [Source:ZFIN;Acc:ZDB-GENE-050517-2]
Coordinates
chr3:12527221-12527675:+
Coord C1 exon
chr3:12527221-12527440
Coord A exon
chr3:12527441-12527516
Coord C2 exon
chr3:12527517-12527675
Length
76 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
CCCTTTATGTTTTCTCCCAGAGC
3' ss Score
10.43
Exon sequences
Seq C1 exon
GTGGTCTTCAGAGTGTTCTCAGTGAAGGCGTTTGTAGCCCAAAACCACCTGGTGGATGTTCTGTTCTTGCTGCTTCTGTACGGCTGGGCGGTGATTCCTCTCATGTACTTGATGAGTTTCCTGTTTTCCACGGCCGCCACAGCCTACACGCGCCTCACCATCTTCAACATCATCAGCGGCACCGCCACCTTCCTCGCCGTCACCATCATGACCATACCTG
Seq A exon
GTGAGACACGCACGTCCCCATTTTAGTTTTGTGCCTTGCAAGAACATCTTTTCACTCCCTTTATGTTTTCTCCCAG
Seq C2 exon
AGCTGAATTTGCTCCATCTCTCGCACCTCCTGGATAAGGTCTTCCTGATCTTCCCGAATTACTGCCTGGGCATGTCCTTCACTGAGTTCTACCAGAACTACGAGATGATCACCTTCTGCACCTCCAGCCCCTTAGCGAAGTACATCTGCAAGTACTACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000100524:ENSDART00000165980:11
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(18.3=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(13.3=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:
AGTTTCCTGTTTTCCACGGCC
R:
CCCAGGCAGTAATTCGGGAAG
Band lengths:
176-252
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]