HsaINT0000638 @ hg19
Intron Retention
Gene
ENSG00000167972 | ABCA3
Description
ATP-binding cassette, sub-family A (ABC1), member 3 [Source:HGNC Symbol;Acc:33]
Coordinates
chr16:2378454-2379855:-
Coord C1 exon
chr16:2379649-2379855
Coord A exon
chr16:2378759-2379648
Coord C2 exon
chr16:2378454-2378758
Length
890 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TGATGTTGGGTTTGGATCAGCCA
3' ss Score
1.46
Exon sequences
Seq C1 exon
GTGCTGGAGAGTCATGCCTGTGAGCCCTGGGCACCTCCTGATGTCCTGCGAGGTCACGGTGTTCCCAAACCTCAGGGTTGCCCTGCCCCACTCCAGAGGCTCTCAGGCCCCACCCCGGAGCCCTCTGTGCGGAGCCGCCTCCTCCTGGCCAGTTCCCCAGTAGTCCTGAAGGGAGACCTGCTGTGTGGAGCCTCTTCTGGGACCCAG
Seq A exon
GTGAGTTCCCTGGTACTGCCCTGCAGCCTGTGTGGGAAGGGGGGTGGTCTATCTTTCTGACCTTCTCTCCCAGCCCTGGGACTGGAGAGGACAAGATTAAGCATGGGGATCTTTCCTTTCTTGGCCAGACTTCCAGTAAGGGAGGTTGTCTGTTCCTCTAACCAGAAGACTTCTTTGAACTGTGACGGTTTTATATTCCTCACTTGGTAGAGGCAGAACGTTCATCTCAGCCAACCCCACGCCCATCTGGAGTGTACTTCCCCGGGATGATGGCCCCAAATGGAGGCACCGGCCTCTTCTTTTTGCCTAAACCACTTCTAGAAACCTTTTATAAACCACAGGCCTTAATGTGTATCTTTAAGTCACTGCTGTTTTATTCATCATCAGCAACTGACTTTGAGACAGGTCTTCTACCTTATTAATTTTAAAAGAATTGGGATAATTTATTAAGTTGCCCCTTAATAGCACTTCATACTATTTTAGCTTTAATTTCTTCACTTTTTAACAATATGATTCATTAAAAGTCATATTTTAAATTAATTTTTAACTGTTTGCAGTTGTATTTCATGTAAATATTTATTGACTACCCTTTAAAGCATAAATTTTGAATATTATTAGATATCAACAGCCACATCTTAAAAAAAAAAAAAAGCAAGAGTTTTAATTTAAAAAGAGCCTTGATATAAATGATTTTCAATGGACTGAAACCAAACCAAAAGTAAAATGGGTCATTTAAAAAAAAAAAAAAACCCTTCCCCGTGCGCTGGAGTCTCCCGGGTCATTGTCGGGGAGCGCTAGCTCATGGTGATCTAGGAATGACTCGCTAATTGTTTGCCTTTCTATCCCGTGCATCTTAACCTGGCTGATGGATGATGTTGGGTTTGGATCAG
Seq C2 exon
CCATGAGTGTGGAGCTGAGCAACTGAACCTGAAACTCTTCCACTGTGAGTCAAGGAGGCTTTTCCGCACATGAAGGACGCTGAGCGGGAAGGACTCCTCTCTGCCTGCAGTTGTAGCGAGTGGACCAGCACCAGGGGCTCTCTAGACTGCCCCTCCTCCATCGCCTTCCCTGCCTCTCCAGGACAGAGCAGCCACGTCTGCACACCTCGCCCTCTTTACACTCAGTTTTCAGAGCACGTTTCTCCTATTTCCTGCGGGTTGCAGCGCCTACTTGAACTTACTCAGACCACCTACTTCTCTAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000167972-ABCA3:NM_001089:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.185
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGAGAGTCATGCCTGTGAG
R:
CAGTCTAGAGAGCCCCTGGTG
Band lengths:
353-1243
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)