HsaINT0000364 @ hg19
Intron Retention
Gene
ENSG00000165029 | ABCA1
Description
ATP-binding cassette, sub-family A (ABC1), member 1 [Source:HGNC Symbol;Acc:29]
Coordinates
chr9:107599261-107599848:-
Coord C1 exon
chr9:107599709-107599848
Coord A exon
chr9:107599378-107599708
Coord C2 exon
chr9:107599261-107599377
Length
331 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGC
5' ss Score
9.85
3' ss Seq
GGCTCCCCACCTGACTCCAGGTG
3' ss Score
5.87
Exon sequences
Seq C1 exon
CTCCTTACTGCAATGATTTGATGAAGAATTTGGAGTCTAGTCCTCTTTCCCGCATTATCTGGAAAGCTCTGAAGCCGCTGCTCGTTGGGAAGATCCTGTATACACCTGACACTCCAGCCACAAGGCAGGTCATGGCTGAG
Seq A exon
GTAAGCTGCCCCCAGCCCAAGACTCCCTCCCCAGAATCTCCCCAGAACTGGGGGCAAAAAACTCAAGGTAGCTTCAGAGGTGTGCGCTAAGTATACTCACGGCTCTTCTGGAATTCCCAGAGTGAAAACCTCAAGTCTGATGCAGACCAGAGCTGGGCCAGCTCCCCAGTCGTGGGTATAGAATCATAGTTACAAGCAGGCATTTCTTGGGGATGGGGAGGACTGGCACAGGGCTGCTGTGATGGGGTATCTTTTCAGGGAGGAGCCAAACGCTCATTGTCTGTGCTTCTCCTCCTTTTTCTGCGGTCCCTGGCTCCCCACCTGACTCCAG
Seq C2 exon
GTGAACAAGACCTTCCAGGAACTGGCTGTGTTCCATGATCTGGAAGGCATGTGGGAGGAACTCAGCCCCAAGATCTGGACCTTCATGGAGAACAGCCAAGAAATGGACCTTGTCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165029-ABCA1:NM_005502:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCTTACTGCAATGATTTGATGA
R:
GACAAGGTCCATTTCTTGGCTG
Band lengths:
254-585
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)