HsaINT0000396 @ hg19
Intron Retention
Gene
ENSG00000165029 | ABCA1
Description
ATP-binding cassette, sub-family A (ABC1), member 1 [Source:HGNC Symbol;Acc:29]
Coordinates
chr9:107645320-107646849:-
Coord C1 exon
chr9:107646708-107646849
Coord A exon
chr9:107645439-107646707
Coord C2 exon
chr9:107645320-107645438
Length
1269 bp
Sequences
Splice sites
5' ss Seq
CATGTAAGT
5' ss Score
8.31
3' ss Seq
TTTTCTTGCACCCTTTACAGTGT
3' ss Score
8.85
Exon sequences
Seq C1 exon
GCCATTTTCCAAATAAAGCCATGCCCTCTGCAGGAACACTTCCTTGGGTTCAGGGGATTATCTGTAATGCCAACAACCCCTGTTTCCGTTACCCGACTCCTGGGGAGGCTCCCGGAGTTGTTGGAAACTTTAACAAATCCAT
Seq A exon
GTAAGTATCAGATCAGGTTTTCTTTCCAAACTTGTCAGTTAATCCTTTTCCTTCCTTTCTTGTCCTCTGGAGAATTTTGAATGGCTGGATTTAAGTGAAGTTGTTTTTGTAAATGCTTGTGTGATAGAGTCTGCAGAATGAGGGAAGGGAGAATTTTGGAGAATTTGGGGTATTTGGGGTATCCATCACCTCGAGTATTTATCATTTCTGTATGTTGTGAACATTTCAAGTCCTGTCTGCTAGCTATTTTGGAATATACTATATGTTGTTAATGATATCATGCAGCAGACGTGCATCTGAATGGGCTGGCTCTAGGAGCTAGAGGGTAGGGGCTGGCACAAAGATGCATGCTGGAAGGGTCCTTGCCCATAAGAAGCTGACAGCCAAGGCTAGGGGAGTTCTGTCTTCTCTGCATCAGGTCACCTCTCTCACCTCTGTCACTGCCCCATCAGACTACAATGTCTGCAGGTCTTTCTCCCCTGAGTGTGAGCTCCCTGAGCAAAGCAGGATGCTGCCCCTTCCCTTTGTATTCCTGGCTCCTGGCTTCAGTGCCTGGACATAAGTATGGGCATAATAAGTGTCCCCCAAATGAGACATTGAGGATTCTTCAAATGCACAGGACCGTGATGTGAGTTAGGACGGAGTAAGGACGATGGGATGTGGCTCAGGACAATCCTGAGGAAGCTGCAGCTGCGGCACGCAGGGCCACACTGTCATGTTCATGGACCCTAGACTGGCTTTGTAGCCTCCATGGGCCCCTTCCATACACAAATATTAAAAATTATATTTCATGACTGCATTGGTATAAAGATGAATATAATCCAGACCAGATTCATGATTATTCATACATTTTTAGTGTATTAACTTTTAATTCTGCTTTTAAAATAAATTAAAACATTCTAATATGCCCTTAAGAGTATCCCAGGCCCAGGCCACTGAGCCTACTGTGGTTCATGGATAAGTTGGCCCTGGGGGCATGTGTGTGCATGCATGTGTGTGCACATGCATGATGAGCCGGGCCTTGAAGGGTGGTAAGATTTGGGTGTGTAGACCAATGGAGAAAGGCATTTGGGGCAGTGATGATGGGTGGGGGAGGGAACATGGTGATGAATGGAGCTGGGTGTGGGGAGCCATGGGAGTGGGTTAGGGCCAGCCTGTGGAGGACCTGGGAGCCAGGCTGAGTTCTATGCACTTGGCAGTCACTTCTGTAAAGCAGCAGAGGCAGTTGGCCTAGCTAAAGCCTTTCGCCTTTTCTTGCACCCTTTACAG
Seq C2 exon
TGTGGCTCGCCTGTTCTCAGATGCTCGGAGGCTTCTTTTATACAGCCAGAAAGACACCAGCATGAAGGACATGCGCAAAGTTCTGAGAACATTACAGCAGATCAAGAAATCCAGCTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165029-ABCA1:NM_005502:4
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:
NO
A:
NA
C2:
NO
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:
TTCCAAATAAAGCCATGCCCTCT
R:
TGAGCTGGATTTCTTGATCTGCT
Band lengths:
254-1523
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)