HsaINT0000888 @ hg38
Intron Retention
Gene
ENSG00000154258 | ABCA9
Description
ATP binding cassette subfamily A member 9 [Source:HGNC Symbol;Acc:HGNC:39]
Coordinates
chr17:68989027-68989930:-
Coord C1 exon
chr17:68989813-68989930
Coord A exon
chr17:68989119-68989812
Coord C2 exon
chr17:68989027-68989118
Length
694 bp
Sequences
Splice sites
5' ss Seq
AAGGTTGGA
5' ss Score
5.64
3' ss Seq
AGCATACCACTTTCTTTCAGGTG
3' ss Score
8.28
Exon sequences
Seq C1 exon
ACACCCGTCATCATTGCCAGCTGTCTACGGAAGGAATATGCAGGCAAAAAGAAAAATTGCTTTTCTAAAAGGAAGAAAAAAATTGCCACAAGAAATGTCTCTTTTTGTGTTAAAAAAG
Seq A exon
GTTGGAAACAGTAGTTCCATTAGTAGAGCAATCTTGAATCTGAAGACTGGATTATTCAGGGAATAAGAGTATCTGAATCTGGGGACATCTATTGACAAACGCAGCAGGCTAAGCCTGCTCCTCCTGCTTAAAAGCCTCAGTTGAAATGATAACGACCTTTTTTTCTTTACATAGGAAGACAGTTATGTCTGTTCTGTAACACAAACAAACAGAACAACAACAATGAAAAGAGGCGGTCTTTCTGTTAAGAAGGATGGTATAGTTTTTAGGTAACAATGTTATTGCAGCGAATACTACACAGAAGGGAGCCAATGGAGGCATAACAGTGCTTTCTCCATTCCCCCAAAACAGCCCATTTCGTGAAAGTGGGGGGTTCGTACAACAGGCTTTGAAATCAAAATATGTTACAACTTCCAGCTCAGCCTCTTACTGTCTGTATGACATGGGGCAACTTATTTATCCTCTTTAAGTCTTAGCTTCCTCACCTGTAAAATGAAGCTAGTTATAATGCTCAGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGGAATAAGGGAAATAATATATATAGCACATTTCACATAGCACTTGACACACAGCCCTCAAATGGTATTTGCTTTTATTTTTGTTGCAATTATTTGTATATTTCTGAGCATACCACTTTCTTTCAG
Seq C2 exon
GTGAAGTTATAGGACTGTTAGGACACAATGGAGCTGGTAAAAGTACAACTATTAAGATGATAACTGGAGACACAAAACCAACTGCAGGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000154258:ENST00000340001:30
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=0.194
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=PU(7.1=25.0)
A:
NA
C2:
PF0000522=ABC_tran=FE(21.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGTCATCATTGCCAGCTGTC
R:
CTGTCCTGCAGTTGGTTTTGTG
Band lengths:
206-900
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development