HsaINT0000591 @ hg19
Intron Retention
Gene
ENSG00000107331 | ABCA2
Description
ATP-binding cassette, sub-family A (ABC1), member 2 [Source:HGNC Symbol;Acc:32]
Coordinates
chr9:139910414-139910923:-
Coord C1 exon
chr9:139910743-139910923
Coord A exon
chr9:139910627-139910742
Coord C2 exon
chr9:139910414-139910626
Length
116 bp
Sequences
Splice sites
5' ss Seq
CATGTGAGT
5' ss Score
7.83
3' ss Seq
GACCCCGCCCACCTACCCAGGTC
3' ss Score
6.11
Exon sequences
Seq C1 exon
AGGAGACCCGTGGCATGGAGGAGGAGCCCACCCACCTGCCTCTGGTTGTCTGCGTGGACAAACTCACCAAGGTCTACAAGGACGACAAGAAGCTGGCCCTGAACAAGCTGAGCCTGAACCTCTACGAGAACCAGGTGGTCTCCTTCTTGGGCCACAACGGGGCGGGCAAGACCACCACCAT
Seq A exon
GTGAGTGTCGGAGGGGCAGGGCGGTGGGCATCTGCTGACCAGAGCAGGAGTCCTAGTCAGGGCAGGGTGGGGCCCCTGCAGAGGGCGTGGGGTCATGACCCCGCCCACCTACCCAG
Seq C2 exon
GTCCATCCTGACCGGCCTGTTCCCTCCAACGTCGGGTTCCGCCACCATCTACGGGCACGACATCCGCACGGAGATGGATGAGATCCGCAAGAACCTGGGCATGTGCCCGCAGCACAATGTGCTCTTTGACCGGCTCACGGTGGAGGAACACCTCTGGTTCTACTCACGGCTCAAGAGCATGGCTCAGGAGGAGATCCGCAGAGAGATGGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107331-ABCA2:NM_001606:20
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.082 A=NA C2=0.000
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
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCTCTACGAGAACCAGGTGG
R:
TGCTCTTGAGCCGTGAGTAGA
Band lengths:
243-359
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)