HsaINT0000399 @ hg19
Intron Retention
Gene
ENSG00000165029 | ABCA1
Description
ATP-binding cassette, sub-family A (ABC1), member 1 [Source:HGNC Symbol;Acc:29]
Coordinates
chr9:107554217-107555187:-
Coord C1 exon
chr9:107555067-107555187
Coord A exon
chr9:107554280-107555066
Coord C2 exon
chr9:107554217-107554279
Length
787 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
TTACATTTTGTTTGTTGCAGATA
3' ss Score
11.02
Exon sequences
Seq C1 exon
ACCTGTAAATGCAAAGCTATCTCCTCTGAATGATGAAGATGAAGATGTGAGGCGGGAAAGACAGAGAATTCTTGATGGTGGAGGCCAGAATGACATCTTAGAAATCAAGGAGTTGACGAAG
Seq A exon
GTGAGAGAGTACAGGTTACAATAGCTCATCTTCAGTTTTTTTCAGCTTTATGTGCTGTAACCCAGCAGTTTGCTGACTTGCTTAATAAAAGGGCATGTGTTCCCAAAATGTACATCTATACCAAGGTTCTGTCAATTTTATTTTAAAAACACCATGGAGACTTCTTAAAGAATTCTTACTGAGAATTCTTTTGTGATATGAATTCCCATTCTCGAATACATTGGTTTTATATGCTTACATTTATGTGTTAGTTATTAAAACATACTAATATTGTATATCTAGTCAAAACTGAGGTAGAGAGAATAAATGGTTGATTTTGAGTTTGAGTTTCATAGTCCAAAAAGCTGATATATTGCCTGTGTTCAAGAGGGTCTATATCAGCCCTCTAGATGCCAGCATCTCCAAATTTTACTTTTTTGGAATCTGTACAGTATTTGCAATATTTTTATTACAAATTTCTACTCTGTGGAATTTAATTTTTAAAATACCTGCAATACATATATATGTTGAATAGATGAAAAATTATGTAGATAATAATGAATGATACGGTTCTAAAAAGACAGGTTAAAAAGTAAGTTCACTTTTATTTTGAGCTTCAGAATCATTCAGAAGCCAGTCGCCACAAACGCAGACCAAGGCTCTTGGCACATCAAATATGCCTATGGCTTAGGGTTATTGACAAGTCTTATGTTGCAGTGTATGTGGTTTATAGTCCTGCCTTCCACAGTTGCTTGGGAGAGCTGTGAGTCACTGAGGCTTATGAATGTTTACATTTTGTTTGTTGCAG
Seq C2 exon
ATATATAGAAGGAAGCGGAAGCCTGCTGTTGACAGGATTTGCGTGGGCATTCCTCCTGGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165029-ABCA1:NM_005502:42
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.195 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=PU(10.3=36.6)
A:
NA
C2:
PF0000522=ABC_tran=PU(7.6=52.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCTGTAAATGCAAAGCTATCTCCT
R:
CTCACCAGGAGGAATGCCCA
Band lengths:
184-971
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)