HsaINT0000868 @ hg19
Intron Retention
Gene
ENSG00000154258 | ABCA9
Description
ATP-binding cassette, sub-family A (ABC1), member 9 [Source:HGNC Symbol;Acc:39]
Coordinates
chr17:67023781-67024786:-
Coord C1 exon
chr17:67024676-67024786
Coord A exon
chr17:67023957-67024675
Coord C2 exon
chr17:67023781-67023956
Length
719 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TCTCTGCCTTCTGCTTTCAGGTT
3' ss Score
12.99
Exon sequences
Seq C1 exon
GTGTGGTGTTTGACATATATGAAGGCCAGATCACTGCCCTCCTTGGTCACAGTGGAGCTGGAAAAACTACCCTGTTAAACATACTTAGTGGGTTGTCAGTTCCAACATCAG
Seq A exon
GTAAGAAGACAGTTATCCAAGGACAAGTACCTGGACAAACACATTAATATGCATTTAATTATTTAACTGGGGCTGGGCACGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAAGCCGAGGCAGGTGGATCATGAGGTCAAGAGATGGAGACCATCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATATAAAAATTAGCCAGGCATGGTGGCAGGTGCCTGTAGGCCCAGCCACTCAGGAGACTGAGGCAGGAGAATCACTTGAACCTGGGAGGCGGAGGTTGCAGTGAGCCTAGATCGTGCCACAGCACTCCAGCCTGGCGACAGAGTGAGACTCCATCTCCAAAAAAAAATTATGTAATTGGTTTTATTAATTAACTTCAATAGTTTCATTACTCATTATATAAGAGAAAAATTTTAGAAGTTTTTCTTATTCTTTTATTGAATTGTATTATACCTATTTAGAAAAATGTTGTTCGTGTTTTAAATATGTCATAAATAGTTTTATGGTTATTAAGTTACTAAGTAGCATTCCAGCTAGATCAGATGTTATTGTGAACATTACATTTTTAATCAGTTCATTGCATATTCCTTACAAGTAAACAATGTTGAAATGAATCTAATAATTGACATACAGTGTTTTCCATTTTAAAAGATCTTCAATGAAGCATGACACATTTTCCTGATGGTCACTCTCTGCCTTCTGCTTTCAG
Seq C2 exon
GTTCAGTCACTGTCTATAATCACACACTTTCAAGAATGGCTGATATAGAAAATATCAGCAAGTTCACTGGATTTTGTCCACAATCCAATGTGCAATTTGGATTTCTCACTGTGAAAGAAAACCTCAGGCTGTTTGCTAAAATAAAAGGGATTTTGCCACATGAAGTGGAGAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000154258-ABCA9:NM_080283:12
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(25.2=100)
A:
NA
C2:
PF0000522=ABC_tran=FE(39.5=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:
GTGTGGTGTTTGACATATATGAAGGC
R:
CACTTCATGTGGCAAAATCCCT
Band lengths:
278-997
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)