HsaINT0000647 @ hg19
Intron Retention
Gene
ENSG00000167972 | ABCA3
Description
ATP-binding cassette, sub-family A (ABC1), member 3 [Source:HGNC Symbol;Acc:33]
Coordinates
chr16:2328944-2331222:-
Coord C1 exon
chr16:2331028-2331222
Coord A exon
chr16:2329132-2331027
Coord C2 exon
chr16:2328944-2329131
Length
1896 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
CGGCTATGCTCCGACCCCAGGTG
3' ss Score
6.84
Exon sequences
Seq C1 exon
GTGTACGAGCAGCGGGTGCCCCTCCTGGCCGTGGACAGGCTCTCCCTCGCGGTGCAGAAAGGGGAGTGCTTCGGCCTGCTGGGCTTCAATGGAGCCGGGAAGACCACGACTTTCAAAATGCTGACCGGGGAGGAGAGCCTCACTTCTGGGGATGCCTTTGTCGGGGGTCACAGAATCAGCTCTGATGTCGGAAAG
Seq A exon
GTGGGTGCAGCCAGGGAGGCTCTGAAGGGGTGAGACAGGCATGGCTGGAGGGGGCACCCTGGAGGCAGGGACAGAGGGATGCTGTCCCCAAACAGCTGCTGCATCTGTGGCTTGAAATGGGCCCAGCACATGCCTCTGGACAGCGAGACAAGGTAATGAGCTAAAGCTAAGCTTCGCCAGAACTAGCAGGTGATGGGAGGGGAGAGAGATGGGTGCCAACATCCGTGAGCCCAGAGAGGCGCATTCAGCACTGACAGCCACCTCTGTGCAGAGGCCATTCTGTGTCCAGGCAGCTCAGGTGTGGGGTTAGAGGCCTTGCTGAGTGAAGGGATGGAAGGCCCTGGGCCCGCCCAGCTTTCCCATGTTGAGCTGAGCCCCACCAGCTCCCCCGCAGAAGGACCAGAGGCAGCCCTCCTGCACCTCTGCCCGGGGCCTGCATGGGAATTCAAGTGTGCCAAGCAGAGCAGGGGAAATGGTAAGCAGGGCCTGGGGCTGAGAAGTGGCCGCGGAGTCCTCTCCTGAGCTCACACCAGGGGTGCCTGGACAGCAGAGGCCCTGGGCCAGAGCACATGCAGGCCCTCTCGGGAGGAAAGCCTCATCCTAGGCTGCAGACTCCCCCATAGAGGGTTCCAGGGCTTACAGGCAATGCACAGCAAACAAACAGAGGAGATGGTACCATGGCTGGAAGCAATAGACACAGGCCCCATGGGGGGACAAGCACATAGGCGTTAGATCTGCATCATCAGGCCAGATTATAAAAGATTATAAACTCACTGTGTCTACAGAAATAAATTATGCAATTGAAAATCTATGCAGGGGAGAGAAAACCGTATGTGATCTAGCAATGGAGGAGAGGGTGAGAAGTCCCCAGTACATGTAATCTGAGTTCCAGAAGGAAGAGAGAGAGAGAGTGGCAGGGGGTAGTAGCCAAAAAGGTAGTGGCTAAGACTTTCCCCAAACTGATTAAAAACAGATTCTGGGCTGGGAGCGTGGCTCACGCCTATAATCCCAGCTTTGGAAGGCCAAGGCAGGCAGATCACTTGAGGTCTAGAGTTCGAGACCAGCCTGGCCAACATGGCAAAATGCTGTCTCTACCAAAGAAAAATACAAAAATTAGCAGGGCATGGTGGCAGGTGCCTATAATCCTAGCTACTCGGGAGCCTGAGGCATGAGAATCACTTGAGCCTGGGAGGCAGAGGTTGTAGTGAGCCGAGATCATGCCACTGCGCTCTACCAGTGTAAGGGAGACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAAAAAATTCTGGAAGCTTGAGAACCCCAAAGAAGGAAGGTAAAGAAAAAGAAATCCAGTCTCTGGAATCCACAGAACCCAGGCACTCCTGCCCCCGACCAGCTGCTGAAGGTAGCTAAGCAGATGGCAGCAGGCACGTCTTAATTCAGCTGGACGTGGTCACTTGTGCAGAGAACAGCTGCTGCACCATCTGACCAAGCAGTACTCACCCCAAACGTGGTGCCCACAAATCTTTCTTCTTAGAGGGAGAAGAAAGAGTCCTAGCACATCAGATGTCCCAGGTGTGAATGAGTGGGTAGCCAGCTCTGAGTCTGCTTCTACGTAAAGGCCATTCTTGCACCACCTAACCCCATGGCTGCCTGTCCTGGACCAGGCTCTGAGAGCAGCTCTGGAAGCCTCCCTGCACCAGGCACATCCTTCCTGTGTCCCTGTTCCAAGAGCTTCCACTGTGGGCAGCCACCACGGCCTGTGCATAGCTCCAGCGCCCCCGTGTACACACACTGGCAGGAACCACAGACAGGCGCAGTGGTGGGCACCTCAAGGGTAGTCCCCGTGGTCCTCTGGAGGAAGGAGGCTTCCCTCCAACCCGCCTCCCTCCCCGGCTATGCTCCGACCCCAG
Seq C2 exon
GTGCGGCAGCGGATCGGCTACTGCCCGCAGTTTGATGCCTTGCTGGACCACATGACAGGCCGGGAGATGCTGGTCATGTACGCTCGGCTCCGGGGCATCCCTGAGCGCCACATCGGGGCCTGCGTGGAGAACACTCTGCGGGGCCTGCTGCTGGAGCCACATGCCAACAAGCTGGTCAGGACGTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000167972-ABCA3:NM_001089:28
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.015 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=PU(37.2=83.1)
A:
NA
C2:
PF0000522=ABC_tran=FE(42.8=100)
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:
GTGGACAGGCTCTCCCTCG
R:
CTGTACGTCCTGACCAGCTTG
Band lengths:
353-2249
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)