HsaINT0000640 @ hg19
Intron Retention
Gene
ENSG00000167972 | ABCA3
Description
ATP-binding cassette, sub-family A (ABC1), member 3 [Source:HGNC Symbol;Acc:33]
Coordinates
chr16:2336695-2338330:-
Coord C1 exon
chr16:2338027-2338330
Coord A exon
chr16:2336969-2338026
Coord C2 exon
chr16:2336695-2336968
Length
1058 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGG
5' ss Score
10.48
3' ss Seq
ACTCTGCCATTGCTCCCCAGGTG
3' ss Score
9.92
Exon sequences
Seq C1 exon
CTCGCCCTGCACTGCCAGCAATTCTGGGCCATGTTCCTGAAGAAGGCCGCATACAGCTGGCGCGAGTGGAAAATGGTGGCGGCACAGGTCCTGGTGCCTCTGACCTGCGTCACCCTGGCCCTCCTGGCCATCAACTACTCCTCGGAGCTCTTCGACGACCCCATGCTGAGGCTGACCTTGGGCGAGTACGGCAGAACCGTCGTGCCCTTCTCAGTTCCCGGGACCTCCCAGCTGGGTCAGCAGCTGTCAGAGCATCTGAAAGACGCACTGCAGGCTGAGGGACAGGAGCCCCGCGAGGTGCTCG
Seq A exon
GTAAGGGGCATCCCGGGGGCGGGACGGGGGCATCGGGGGCCAGTCCTGCAGCCAGAGTTCGCCTTCCTGACTGCAGCAGGGTCGACATCTGGGGAGGATGGTTCTTGGCTGTTCCGAATGTACTGAGGGAGGTTCAGCAGCATCCCTGACCTTGCCCCACCCCATCATGACCATCAAACATGCCTGGAAACATTGCGGATGTCCCCTGGGTGGCAGATCACGGCACTGAGTCAGGGGAAGTGCCCTGGAGGTGCCAGAGACACTGGCATCCTGGGGCCAGGCTTTGTCAGGCGTCTTTTTACTGAAGCTGTGTCTTTCAGGATCATTCATGGGCAAAATGCAGAAGCATAGTGACTTCAAGTTACCTTTGCTTTGTGATGATGCTGGCCACAGTGTGCCTTCGTGTGACAGGGTGTTTTCTTTCAACATCTTAAAACTCACAGTTCTTGGCCAGGCACAGTAGCTCACACCTGTCATCCCACTACTTTGGGAGGCCGAGGCAGGTGGATCACTTGAGGTCAGGAGTTCGAGACCAGCCTGGTCAACATGGCAAAACTCTGTCTCTACTAAACACAAAAATTAGCTAGGTGTGGTGATGGGTACCTGTAATCCCAGCTACTCTGGAGGCTGAGGCAGGAGAATGGCTTGAACCTGGGCGGTGGAGGCTGCAGTGAGCCAAGATCGCACCATTGCACTCCAGCCTGGGTGACAGAGCAAGACTGTCTCAAAAAAAAAAAGAAAGAGTCTTGGTAGTCATAGTTGGATACTGCCCCAGGCTCAGAACAGGGACCGTGCTCTGGTTAATGGAACCTACTGGAAGGTTTTCTTATTTTGCAGCTCCTTTCCCGGTTCCTGACTGGCATTCAAAGTTCCACATACTGAATGATGACAAAACCTTGCCAGAAATTATACTCTCCTTAGGAGAAGGGTGATGGGGCGGGCAGCTCAGAGGATGCTGGCACCACTCTATTGGGTCCCTGATTAGCCATGCTCAGGTGGCAGGGGGTGCCCAGGTGTCACCTCTTCCTGTGTCCCCTGACTCTGCCATTGCTCCCCAG
Seq C2 exon
GTGACCTGGAGGAGTTCTTGATCTTCAGGGCTTCTGTGGAGGGGGGCGGCTTTAATGAGCGGTGCCTTGTGGCAGCGTCCTTCAGAGATGTGGGAGAGCGCACGGTCGTCAACGCCTTGTTCAACAACCAGGCGTACCACTCTCCAGCCACTGCCCTGGCCGTCGTGGACAACCTTCTGTTCAAGCTGCTGTGCGGGCCTCACGCCTCCATTGTGGTCTCCAACTTCCCCCAGCCCCGGAGCGCCCTGCAGGCTGCCAAGGACCAGTTTAACGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000167972-ABCA3:NM_001089:21
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.010 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=PU(19.7=77.5)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(22.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGGGCCATGTTCCTGAAGA
R:
CCACAAGGCACCGCTCATTAA
Band lengths:
354-1412
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)