HsaINT0000583 @ hg19
Intron Retention
Gene
ENSG00000107331 | ABCA2
Description
ATP-binding cassette, sub-family A (ABC1), member 2 [Source:HGNC Symbol;Acc:32]
Coordinates
chr9:139912425-139912803:-
Coord C1 exon
chr9:139912630-139912803
Coord A exon
chr9:139912528-139912629
Coord C2 exon
chr9:139912425-139912527
Length
102 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGG
5' ss Score
7.13
3' ss Seq
ATGGCTGCCCCCACCCACAGACA
3' ss Score
8.79
Exon sequences
Seq C1 exon
GTGTGATCTTCCAGACCCGGAAGGACGGCTCGCTCCCGCCTCACGTGCACTACAAGATCCGCCAGAACTCCAGCTTCACCGAGAAAACCAACGAGATCCGCCGCGCCTACTGGCGGCCTGGGCCCAATACTGGCGGCCGCTTCTACTTCCTCTACGGCTTCGTCTGGATCCAGG
Seq A exon
GTGAGGAGCAGGCCCGGAAGACCGGCTGGAGGATTCATGGGGGAGGACAGGTGTGAGGACGAGAGGGCCTGCCCGGCACCTGATGGCTGCCCCCACCCACAG
Seq C2 exon
ACATGATGGAGCGCGCCATCATCGACACTTTTGTGGGGCACGATGTGGTGGAGCCAGGCAGCTACGTGCAGATGTTCCCCTACCCCTGCTACACACGCGATGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107331-ABCA2:NM_001606:13
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.017 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF126982=ABC2_membrane_3=PU(7.7=51.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGATCTTCCAGACCCGGAA
R:
GGGAACATCTGCACGTAGCTG
Band lengths:
252-354
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)