HsaINT0000642 @ hg19
Intron Retention
Gene
ENSG00000167972 | ABCA3
Description
ATP-binding cassette, sub-family A (ABC1), member 3 [Source:HGNC Symbol;Acc:33]
Coordinates
chr16:2334780-2335647:-
Coord C1 exon
chr16:2335443-2335647
Coord A exon
chr16:2335000-2335442
Coord C2 exon
chr16:2334780-2334999
Length
443 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGC
5' ss Score
8.05
3' ss Seq
GCCTCCCTGTGCCGCCGCAGGTG
3' ss Score
8.97
Exon sequences
Seq C1 exon
GGGCCGGAAGGGATTCGACATTGCCCTCAACCTGCTCTTCGCCATGGCATTCTTGGCCAGCACGTTCTCCATCCTGGCGGTCAGCGAGAGGGCCGTGCAGGCCAAGCATGTGCAGTTTGTGAGTGGAGTCCACGTGGCCAGTTTCTGGCTCTCTGCTCTGCTGTGGGACCTCATCTCCTTCCTCATCCCCAGTCTGCTGCTGCTG
Seq A exon
GTGAGCGCCGGAGGGTGCTGGATCCGTTCCCCTGCAGACCGCAGAGGGCTTGCCCTGGGACCCCTGTGCAGAACCGGAACCAGCTGGGCAGCCCCTAGGCCGGCAGCTCGGCCCGACTCAGGGAGGACAGCTGGAATCCCCTGGCGGCTGCCCCCTCGCCTCCTCCCTGCACCCTCAGCCTTTACCCTCCATGCATGGGCAGCACCCGGAGCAGCCATCCTGGTTACAGCTCCGGGTGCAAGGGGACGAGGGGAAACTGGGACAGAGAGGGTCCTGGGGCTGAAAGCCACCGCGGGGGCCAGACGTGGCCTGTGGGGCTGATGGACATGGGCCAGCTGACCGGGAGGGGTCTGAGGACCTCCAAATGCTCCTCTCACCCCTTCCCTACCCGTGAGCTCCTCTCAGCTTGGCATGCACAGCAGCGCCTCCCTGTGCCGCCGCAG
Seq C2 exon
GTGGTGTTTAAGGCCTTCGACGTGCGTGCCTTCACGCGGGACGGCCACATGGCTGACACCCTGCTGCTGCTCCTGCTCTACGGCTGGGCCATCATCCCCCTCATGTACCTGATGAACTTCTTCTTCTTGGGGGCGGCCACTGCCTACACGAGGCTGACCATCTTCAACATCCTGTCAGGCATCGCCACCTTCCTGATGGTCACCATCATGCGCATCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000167972-ABCA3:NM_001089:23
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:
PF126982=ABC2_membrane_3=FE(16.9=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(18.2=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:
CATTGCCCTCAACCTGCTCTT
R:
TGAAGATGGTCAGCCTCGTGT
Band lengths:
353-796
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)