HsaINT0000382 @ hg19
Intron Retention
Gene
ENSG00000165029 | ABCA1
Description
ATP-binding cassette, sub-family A (ABC1), member 1 [Source:HGNC Symbol;Acc:29]
Coordinates
chr9:107574855-107576512:-
Coord C1 exon
chr9:107576399-107576512
Coord A exon
chr9:107575004-107576398
Coord C2 exon
chr9:107574855-107575003
Length
1395 bp
Sequences
Splice sites
5' ss Seq
CAGGTCTGT
5' ss Score
6.84
3' ss Seq
TCAGTGTTGGCTTCTTGCAGAAT
3' ss Score
7.57
Exon sequences
Seq C1 exon
ATGGTACCTTGCCAGCAAGACGAAACAGGCGGGCCTTCGGGGACAAGCAGAGCTGTCTTCGCCCGTTCACTGAAGATGATGCTGCTGATCCAAATGATTCTGACATAGACCCAG
Seq A exon
GTCTGTTAGGGCAAGATCAAACAGTGTCCTACTGTTTGAATGTGAAATTCTCTCTCATGCTCTCACCTGTTTTCTTTGGATGGCCTTTAGCCAAGGTGATAGATCCCTACAGAGTCCAAAGAGAAGTGAGGAAATGGTAAAAGCCACTTGTTCTTTGCAGCATCGTGCATGTGATCAAACCTGAAAGAGCCTATCCATATCACTTCCTTTAAAGACATAAAGATGGTGCCTCAATCCTCTGAACCCATGTATTTATTATCTTTTCTGCGGGGTCCTAGTTTCTTGTATACATTAGGTGTTTAATTGTTGAACAAATATTCATTCGAGTAGATGAGTGATTTTGAAAGAGTCAGAAAGGGGAATTTGCTGTTAGAGTTAATTGTACCCTAAGACTTAGATATTTGAGGCTGGGCATGGTGGCTCATGCCAGTAATCCCAGCGCTTTGAGAGGCTGAGGTGGGTAGATCACCTGAGGTCAGGAGTTTGAGACCAGTCTGACCAACAAGGTGAAACCCCGTCTCTACTAAATACAAAAAATTAGCCGAGTGTGGTGGCACATGCCTGTCATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCAGGAGGCAGAGGTTGCAGTCAGCCACGGTTGCGCCATTGCACTCCAGACTGGGCAACAAGAGTGAAAACTCCATCTCAAAAAAGAAAAAAAAAGAATTAGATATTTTGGATGAGTGTGTCTTTGTGTGTTTAACTGAGATGGAGAGGAGAGCTAAGACATCAAACAAATATTGTTAAGATGTAAAAGCACATCAGTTAGGTATCATTAGTTTAGGACAAGGATTTCTAGAAAATTTTTAGGAACAGAAAACTTTCCAGTTCTCTCACCCCTGCTCAAAGAGTGTATGGCTCTTACATTATATATAACTGCCTGACTTCATACAGTATCAGTACTTAGATCATTTGAAATGTGTCCACGTTTTACCAAAATATAATAGGGTGAGAAGCTGAGATGCTAATTGCCATTGTGTATTCTCAAATATGTCAAGCTACGTACATGGCCTGTTTCATAGAGTAGTCTATAAGAAATTGATGACTTGATTCATCCGAATGGCTGGCTGTAACACCTGGTTACGCATGAACACCTCTTTTCAGTTGTCTCAAGACACCTTTCTTTTCTGTACTTATCAGACAAGGACTGAAAGGCAGAGACTGCTACTGTTAGACATTTTGAGTCAAGCTTTTCCTTGGACATAGCTTTGTCATGAAAGCCCTTTACTTCTGAGAAACTTCTAGCTTCAGACACATGCCTTCAAGATAGTTGTTGAAGACACCAGAAGAAGGAGCATGGCAATGCCGAAAACACCTAAGATAATAGGTGACCTTCAGTGTTGGCTTCTTGCAG
Seq C2 exon
AATCCAGAGAGACAGACTTGCTCAGTGGGATGGATGGCAAAGGGTCCTACCAGGTGAAAGGCTGGAAACTTACACAGCAACAGTTTGTGGCCCTTTTGTGGAAGAGACTGCTAATTGCCAGACGGAGTCGGAAAGGATTTTTTGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165029-ABCA1:NM_005502:27
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.513 A=NA C2=0.140
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF126982=ABC2_membrane_3=PU(1.1=12.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGCCAGCAAGACGAAACAGG
R:
AAATCCTTTCCGACTCCGTCTG
Band lengths:
246-1641
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)