HsaINT0000875 @ hg19
Intron Retention
Gene
ENSG00000154258 | ABCA9
Description
ATP-binding cassette, sub-family A (ABC1), member 9 [Source:HGNC Symbol;Acc:39]
Coordinates
chr17:67014554-67016727:-
Coord C1 exon
chr17:67016529-67016727
Coord A exon
chr17:67014721-67016528
Coord C2 exon
chr17:67014554-67014720
Length
1808 bp
Sequences
Splice sites
5' ss Seq
TATGTGAGT
5' ss Score
5.56
3' ss Seq
TTACATTTTCCTCTGCATAGATT
3' ss Score
8.26
Exon sequences
Seq C1 exon
ATATTGGAATTTGGGGACAATTACAAACTGATGGGGCAAAAGATATAGGAAGCCTTGTTGAGCTGGAACAAGTTTTGTCTTCCTTCCACGAAACAAGGAAAACAATCAGTGGCGTGGCGCTCTGGAGGCAGCAGGTCTGTGCAATAGCAAAAGTTCGCTTCCTAAAGTTAAAGAAAGAAAGAAAAAGCCTGTGGACTAT
Seq A exon
GTGAGTATCTGAGTGTTTCAGATTTGTTTTGTCTGTGAACTAAAAATAAATTTAAGAGAGCAAAACATAAAAGAAACTCAGATAAAATAAATTTCAGTAAATGCACATTGTCTTTTAAACAAAGAAATCATTTTTTAATTAAAGAAACCATTTTTAATCATGTGGATATATAATTAAAACAGATACGGGTTGGGATTGTTCTTTTTTTAAATTTCACACAGATTTTGTTTTTACCAATGGGTTGAAGTAGTTCTTCAAAAGCACGTGGATATTAGTACTTAGGTCCCATCCTAAAGACCCATTTCCTCTTTTCCCAAGGTATCAAAATCTGTAGCTGTCAGGGTTCCCCAGGGAAATGAAACCAATAGGATATACATATATAAACATACTTACTTTAAGGAATTTCATTATGTAATTGTGGGGCTTGGCAAATCTGAAATCCACAAGGCAGAACACCAGGCTGGAAACTTGGGTTAGAGTTAATGCTGTAGTTGGAAGACTGGAAACTTGGGTTAGAGTTAATGTTGTAGTTGGAAGACTGGAAACTTAGGCACAATTTCCATGTTACAGTCTTGAGGCTCTATAAAAGAGTCTGCCTTGGCTTCACGATCATATCTGGAACCCACTATAAGGTTCACATGTACCCCCAGAGCTTCAGCCTTATCATCAGGAACACTCATTCACTGAGAACATTCATTCATCCAAAAATATTAGTGAGCACCTCTATGCAACACTCTATTATTAAGTGATTATAACATATATCAAAAGAAATCAGACATGACAGTCCACCCTTGAGGGTGATTAGACATATAGTAAATAACAGACAATCCTGTGAACTATGGCATTTAGTAGGAGGGAGATTATGTCAAAATAGAAAGCTCAGGGAGATTTTGAAGAAGAGAGAGGAGAATGGAAATTCAGGCTGAGGGAGTAGTACTGAATATGGGGATACATGAGAAATCTAAAGAACTATTAATCTGAGTTAATTGCAACATAAAGTGTATGAAAAAGTAAAAATATTTTTGAAATATATTCAAAGAGCTAAGGAGTTTGCATTTTATGAATACTAAGGAAGTATTAAGACTGTATTTTTTATTTTCAATAGGTAATTGACATAATGTCAACAAAATGTTAAGAAGCTTAATTGGGTAATTGTGCAAAATTGTTTGGTAATGGTAGAATATGGAGACAATGAAAACAAACATTTAGAACAATATTGAAGAGTCAGGAAGGAGTTAATAAAAGCCCAACTTAAGAAGAGGAAGAGAGAACAAGGTTTGGAGGCAAGCAATAAAGATGCTATGATAGATATGAATTTCCAAATATTAGAAAATAAACTTAAGGGAGAGAAATGGGTGGAAAATGATTGAGCTCTTGGTGCCCAGGGGAATGAGAAAATGCTGTAATTTACAGAAATTGGAAACAGGATGGGATAAAGTTCAGAGTGTAGTAAGTATGGGTGTTAGTGATATGCCAATTTCAGTAGTGCAGAAAAAGAAAGAAATGCATGACTGAAATAAGGCAATGAGTTAGGGATTGTGAAGAGAGATTTAAGAGTCATAATCCACAGACTTCATAAACCCGAAGCCAAGGTGTCCTGCTTGGCACTTGAGAGAGAGCAAAAGACTAAAGGTAGATACATATGACCCATCTCATTTTAGAAACAAGGAAGTGGGGCAAAGTATGATTCAAATGTTTGGTTATTGATTATAATTTATTTCTGTTATTATATTCATTATACCTTCAAACTTAAAAACCCACAAAAGTTGCTAAAATTATTTTTTTCTTTTACATTTTCCTCTGCATAG
Seq C2 exon
ATTATTGCTTTTTGGTATTAGCTTTATCCCTCAACTTTTGGAACATCTATTCTACGAGTCATATCAGAAAAGTTACCCGTGGGAACTGTCTCCAAATACATACTTCCTCTCACCAGGACAACAACCACAGGATCCTCTGACCCATTTACTGGTCATCAATAAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000154258-ABCA9:NM_080283:19
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:
NO
A:
NA
C2:
PF126982=ABC2_membrane_3=PU(2.3=12.3)
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:
TGGGGACAATTACAAACTGATGGG
R:
AATGGGTCAGAGGATCCTGTGG
Band lengths:
334-2142
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)