HsaINT0000871 @ hg19
Intron Retention
Gene
ENSG00000154258 | ABCA9
Description
ATP-binding cassette, sub-family A (ABC1), member 9 [Source:HGNC Symbol;Acc:39]
Coordinates
chr17:67022518-67023255:-
Coord C1 exon
chr17:67023117-67023255
Coord A exon
chr17:67022609-67023116
Coord C2 exon
chr17:67022518-67022608
Length
508 bp
Sequences
Splice sites
5' ss Seq
CGGGTAATT
5' ss Score
6.79
3' ss Seq
TTTTGATTATTTCTAACTAGACA
3' ss Score
5.82
Exon sequences
Seq C1 exon
GTTTTGCTATTGGATGAACCGACTGCTGGATTGGATCCTCTTTCAAGGCACCGAATATGGAATCTCCTGAAAGAGGGGAAATCAGACAGAGTAATTCTCTTCAGCACCCAGTTTATAGATGAGGCTGACATTCTGGCGG
Seq A exon
GTAATTTTTTGTTTCTCTTATGTATCTTCATGAGAGGTTAGAGACAGTGTGGAATATGAACAGGTATGCTCCACAGCTGTGTCTCCCTGGAACTGCCATGGCCCAAGACAGGAGAATTTTGCTCTTACTCATTTGTGGGTCTGCATGCCAGAGTACTTGGCCCCATGGAAATATTCTGAGCCCATTGCAGAGCAGCTTTCTGGTTGTAAAATACATATCACACTTTCTAAGATACAATTTGTTTTAGGCAGTCTTGATGTCAGTGTAACTGAAACAGATCCTTTAAATGTATAATTTTTCTCAATACGCTAAAGAATAAGTTGACATAATTTATCACTCATTCGAGCTGTTGGATGACAAAAAAAAGTGGTTTACGTATGGCCAGAATTAGAGTATATCTATTTTAGTGTGTCATGCTGCTACAATACATTGTTAATAGATTTGTGTTTTGTGAATAGTAAAGAAATAAGTCCTTCATGTAACTTATCTTTTGATTATTTCTAACTAG
Seq C2 exon
ACAGGAAGGTGTTCATATCCAATGGGAAGCTGAAGTGTGCAGGCTCTTCTCTGTTCCTTAAGAAGAAATGGGGCATAGGCTACCATTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000154258-ABCA9:NM_080283:15
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=PD(5.4=17.0)
A:
NA
C2:
NO
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:
GTTTTGCTATTGGATGAACCGACTG
R:
CTTAAATGGTAGCCTATGCCCCA
Band lengths:
230-738
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
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)