HsaINT0000398 @ hg19
Intron Retention
Gene
ENSG00000165029 | ABCA1
Description
ATP-binding cassette, sub-family A (ABC1), member 1 [Source:HGNC Symbol;Acc:29]
Coordinates
chr9:107555067-107555581:-
Coord C1 exon
chr9:107555452-107555581
Coord A exon
chr9:107555188-107555451
Coord C2 exon
chr9:107555067-107555187
Length
264 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TTCTTGTTTTTTCCCCCAAGACC
3' ss Score
6.98
Exon sequences
Seq C1 exon
GGGAGAATCGCTTTGTGTCACCATTATCTTGGGACTTGGTGGGACGAAACCTCTTCGCCATGGCCGTGGAAGGGGTGGTGTTCTTCCTCATTACTGTTCTGATCCAGTACAGATTCTTCATCAGGCCCAG
Seq A exon
GTGAGCTTTTTCTTAGAACCCGTGGAGCACCTGGTTGAGGGTCACAGAGGAGGCGCACAGGGAAACACTCACCAATGGGGGTTGCATTGAACTGAACTCAAAATATGTGATAAAACTGATTTTCCTGATGTGGGCATCCCGCAGCCCCCTCCCTGCCCATCCTGGAGACTGTGGCAAGTAGGTTTTATAATACTACGTTAGAGACTGAATCTTTGTCCTGAAAAATAGTTTGAAAGGTTCATTTTTCTTGTTTTTTCCCCCAAG
Seq C2 exon
ACCTGTAAATGCAAAGCTATCTCCTCTGAATGATGAAGATGAAGATGTGAGGCGGGAAAGACAGAGAATTCTTGATGGTGGAGGCCAGAATGACATCTTAGAAATCAAGGAGTTGACGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165029-ABCA1:NM_005502:41
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=0.195
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=PD(6.3=75.0)
A:
NA
C2:
PF0000522=ABC_tran=PU(10.3=36.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGAATCGCTTTGTGTCACCA
R:
TCGTCAACTCCTTGATTTCTAAGA
Band lengths:
248-512
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)