HsaINT0000728 @ hg19
Intron Retention
Gene
ENSG00000154265 | ABCA5
Description
ATP-binding cassette, sub-family A (ABC1), member 5 [Source:HGNC Symbol;Acc:35]
Coordinates
chr17:67251684-67251991:-
Coord C1 exon
chr17:67251874-67251991
Coord A exon
chr17:67251776-67251873
Coord C2 exon
chr17:67251684-67251775
Length
98 bp
Sequences
Splice sites
5' ss Seq
AAGGCTGGT
5' ss Score
0.71
3' ss Seq
TTTTCTTTCAATTCCTTTAGGAG
3' ss Score
10.64
Exon sequences
Seq C1 exon
AAACCATCCATTATGGTCAGCAATTTGCATAAAGAATATGATGACAAGAAAGATTTTCTTCTTTCAAGAAAAGTAAAGAAAGTGGCAACTAAATACATCTCTTTCTGTGTGAAAAAAG
Seq A exon
GCTGGTATTTAATTTTTCCTTACATAACTTTTCTAGAAGAGTAATTTCTACTTTTAGTATGATTTGATTATGATTTTTTTTTCTTTCAATTCCTTTAG
Seq C2 exon
GAGAGATCTTAGGACTATTGGGTCCAAATGGTGCTGGCAAAAGCACAATTATTAATATTCTGGTTGGTGATATTGAACCAACTTCAGGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000154265-ABCA5:NM_018672:29
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=PU(6.8=25.0)
A:
NA
C2:
PF0000522=ABC_tran=FE(20.5=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:
TCCATTATGGTCAGCAATTTGCA
R:
ATTAATAATTGTGCTTTTGCCAGC
Band lengths:
168-266
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)