HsaINT0000614 @ hg19
Intron Retention
Gene
ENSG00000107331 | ABCA2
Description
ATP-binding cassette, sub-family A (ABC1), member 2 [Source:HGNC Symbol;Acc:32]
Coordinates
chr9:139904221-139904576:-
Coord C1 exon
chr9:139904435-139904576
Coord A exon
chr9:139904356-139904434
Coord C2 exon
chr9:139904221-139904355
Length
79 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGG
5' ss Score
8.48
3' ss Seq
CACCTGCGTTCCCTGGCCAGGTG
3' ss Score
10.27
Exon sequences
Seq C1 exon
CGTGCTGAAGGAGCTGCTCCAGGTGCAGCAGAGCCTCGGCTACTGCCCGCAGTGTGACGCGCTGTTCGACGAGCTCACGGCCCGGGAGCACCTGCAGCTGTACACGCGGCTGCGTGGGATCTCCTGGAAGGACGAGGCCCGG
Seq A exon
GTGAGGATCTGTGGGGCGGGGCAGGGAGTCAGCACGCTGGGTGGCCCTGCCTCCACTGACACCTGCGTTCCCTGGCCAG
Seq C2 exon
GTGGTGAAGTGGGCTCTGGAGAAGCTGGAGCTGACCAAGTACGCAGACAAGCCGGCTGGCACCTACAGCGGCGGCAACAAGCGGAAGCTCTCCACGGCCATCGCCCTCATTGGGTACCCAGCCTTCATCTTCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107331-ABCA2:NM_001606:41
Average complexity
IR-S
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=FE(32.4=100)
A:
NA
C2:
PF0000522=ABC_tran=FE(30.3=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:
CTGCGTGGGATCTCCTGGAAG
R:
CAGGAAGATGAAGGCTGGGTAC
Band lengths:
168-247
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)