HsaINT0000870 @ hg38
Intron Retention
Gene
ENSG00000154258 | ABCA9
Description
ATP binding cassette subfamily A member 9 [Source:HGNC Symbol;Acc:HGNC:39]
Coordinates
chr17:69026976-69027449:-
Coord C1 exon
chr17:69027330-69027449
Coord A exon
chr17:69027115-69027329
Coord C2 exon
chr17:69026976-69027114
Length
215 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
AGGACTTTCCTCCTGTCCAGGTT
3' ss Score
7.7
Exon sequences
Seq C1 exon
GTACAACGAGTTGTACAGGAATTAGAAATGGAAAATATTCAAGACATCCTTGCTCAAAACTTAAGTGGTGGACAAAATAGGAAACTAACTTTTGGGATTGCCATTTTAGGAGATCCTCAA
Seq A exon
GTAAGTCAAACAAAAATTACTGGTGAAATCAGATTGAAGACTATAAAATTATTTTATTAGGTCAAACAATTTTCAAATGATAAATGTAAGAGAACTTTTAGGATGAAATATTAAGTACTAACAAGTTTCTCCCAAATACTTTTAAAAGTACAGTGCTTTTTAAAAGGATCTTATCCGAAAGGGTGGAATTACTTTAGGACTTTCCTCCTGTCCAG
Seq C2 exon
GTTTTGCTATTGGATGAACCGACTGCTGGATTGGATCCTCTTTCAAGGCACCGAATATGGAATCTCCTGAAAGAGGGGAAATCAGACAGAGTAATTCTCTTCAGCACCCAGTTTATAGATGAGGCTGACATTCTGGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000154258:ENST00000340001:14
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=0.000
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=FE(26.5=100)
A:
NA
C2:
PF0000522=ABC_tran=PD(5.4=17.0)
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:
ACGAGTTGTACAGGAATTAGAAATGG
R:
CGCCAGAATGTCAGCCTCATC
Band lengths:
253-468
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