HsaINT0000373 @ hg19
Intron Retention
Gene
ENSG00000165029 | ABCA1
Description
ATP-binding cassette, sub-family A (ABC1), member 1 [Source:HGNC Symbol;Acc:29]
Coordinates
chr9:107583656-107584948:-
Coord C1 exon
chr9:107584777-107584948
Coord A exon
chr9:107583788-107584776
Coord C2 exon
chr9:107583656-107583787
Length
989 bp
Sequences
Splice sites
5' ss Seq
CATGTAAGA
5' ss Score
5.58
3' ss Seq
TTCTAAATTTTTGTCCTCAGGTC
3' ss Score
11.14
Exon sequences
Seq C1 exon
TCTGCATGGAGGAGGAACCCACCCACTTGAAGCTGGGCGTGTCCATTCAGAACCTGGTAAAAGTCTACCGAGATGGGATGAAGGTGGCTGTCGATGGCCTGGCACTGAATTTTTATGAGGGCCAGATCACCTCCTTCCTGGGCCACAATGGAGCGGGGAAGACGACCACCAT
Seq A exon
GTAAGAAGAGGGTGTGGTTCCCGCAGAATCAGCCACAGGAGGGTTCTGCAGTAGAGTTAGAAATTTATACCTTAGGAAACCATGCTGATCCCTGGGCCAAGGGAAGGAGCACATGAGGAGTTGCCGAATGTGAACATGTTATCTAATCATGAGTGTCTTTCCACGTGCTAGTTTGCTAGATGTTATTTCTTCAGCCTAAAACAAGCTGGGGCCTCAGATGACCTTTCCCATGTAGTTCACAGAATTCTGCAGTGGTCTTGGAACCTGCAGCCACGAAAAGATAGATTACATATGTTGGAGGGAGTTGGTAATTCCCAGGAACTCTGTCTCTAAGCAGATGTGAGAAGCACCTGTGAGACGCAATCAAGCTGGGCAGCTGGCTTGATTGCCTTCCCTGCGACCTCAAGGACCTTACAGTGGGTAGTATCAGGAGGGGTCAGGGGCTGTAAAGCACCAGCGTTAGCCTCAGTGGCTTCCAGCACGATTCCTCAACCATTCTAACCATTCCAAAGGGTATATCTTTGGGGGGTGACATTCTTTTCCTGTTTTCTTTTTAATCTTTTTTTAAAACATAGAATTAATATATTATGAGCTTTTCAGAAGATTTTTAAAAGGCAGTCAGAAATCCTACTACCTAACACAAAAATTGTTTTTATCTTTGAATAATATGTTCTTGTTTGTCCATTTTCCATGCATGCGATGTTAGGCATACAAAATACATTTTTTAAAGAATACTTTCATTGCAGATTGGAAACTTCGTTTAAAAAATGCTCATACTAAAATTGGCATTTCTAACCCATAGGCCCACTTGTAGTTATTTACCGAAGCAAAAGGACAGCTTTGCTTTGTGTGGGTCTGGTAGGGTTCATTAGAAAGGAATGGGGGCGGTGGGAGGGTTGGTGTTCTGTTCTCTCTGCAGACTGAATGGAGCATCTAGAGTTAAGGGTAGGTCAACCCTGACTTCTGTACTTCTAAATTTTTGTCCTCAG
Seq C2 exon
GTCAATCCTGACCGGGTTGTTCCCCCCGACCTCGGGCACCGCCTACATCCTGGGAAAAGACATTCGCTCTGAGATGAGCACCATCCGGCAGAACCTGGGGGTCTGTCCCCAGCATAACGTGCTGTTTGACAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165029-ABCA1:NM_005502:19
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(18.5=46.6)
A:
NA
C2:
PF0000522=ABC_tran=FE(30.1=100)
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:
TCTGCATGGAGGAGGAACCC
R:
CCAGGTTCTGCCGGATGGT
Band lengths:
270-1259
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)