HsaINT0000588 @ hg19
Intron Retention
Gene
ENSG00000107331 | ABCA2
Description
ATP-binding cassette, sub-family A (ABC1), member 2 [Source:HGNC Symbol;Acc:32]
Coordinates
chr9:139911026-139911576:-
Coord C1 exon
chr9:139911372-139911576
Coord A exon
chr9:139911191-139911371
Coord C2 exon
chr9:139911026-139911190
Length
181 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTG
5' ss Score
9.04
3' ss Seq
CTCCCCTCCCCGACCCCCAGGCA
3' ss Score
8.85
Exon sequences
Seq C1 exon
TCCCTCATGTCCACGACGGCCTTTGGTCTGGGCTCTAAGTACTTCGCGCTGTATGAGGTGGCCGGCGTGGGCATCCAGTGGCACACCTTCAGCCAGTCCCCGGTGGAGGGGGACGACTTCAACTTGCTCCTGGCTGTCACCATGCTGATGGTGGACGCCGTGGTCTATGGCATCCTCACGTGGTACATTGAGGCTGTGCACCCAG
Seq A exon
GTACTGGCCAGCCCTTGGAGGGCAGGGGAGAGGCAGGGGTCCCCAGCCAGGGTTGGGGACCAGCAGTCTGTGTCCACTCCTGGATGCAGCACGGGTGGCTCCCTGGGTGGGCACGTGGCCCACGTGGTGGATGGTCACCCCAGGCCCTAGGTCAGCCTCCCCTCCCCTCCCCGACCCCCAG
Seq C2 exon
GCATGTACGGGCTGCCCCGGCCCTGGTACTTCCCACTGCAGAAGTCCTACTGGCTGGGCAGTGGGCGGACAGAAGCCTGGGAGTGGAGCTGGCCGTGGGCACGCACCCCCCGCCTCAGTGTCATGGAGGAGGACCAGGCCTGTGCCATGGAGAGCCGGCGCTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107331-ABCA2:NM_001606:18
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=0.072
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=PD(26.2=88.4)
A:
NA
C2:
NO
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:
GCCTTTGGTCTGGGCTCTAAG
R:
AGCCAGTAGGACTTCTGCAGT
Band lengths:
242-423
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)