HsaINT0000648 @ hg19
Intron Retention
Gene
ENSG00000167972 | ABCA3
Description
ATP-binding cassette, sub-family A (ABC1), member 3 [Source:HGNC Symbol;Acc:33]
Coordinates
chr16:2328289-2329131:-
Coord C1 exon
chr16:2328944-2329131
Coord A exon
chr16:2328460-2328943
Coord C2 exon
chr16:2328289-2328459
Length
484 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCAC
5' ss Score
4.29
3' ss Seq
TGGCACCCTCCTGCCTCTAGTGG
3' ss Score
6.99
Exon sequences
Seq C1 exon
GTGCGGCAGCGGATCGGCTACTGCCCGCAGTTTGATGCCTTGCTGGACCACATGACAGGCCGGGAGATGCTGGTCATGTACGCTCGGCTCCGGGGCATCCCTGAGCGCCACATCGGGGCCTGCGTGGAGAACACTCTGCGGGGCCTGCTGCTGGAGCCACATGCCAACAAGCTGGTCAGGACGTACAG
Seq A exon
GTGCACCTCCCGAGCCCTGGCCCTTCCCAGAGTGGAGTCAGAATCAAGGTCCCCATAGCATAGAGCTGGGAGTGACCGCTCAGGTCAGCAGCCAGAGCTCCTGCTTGTGGCTCCAGGATGGAGCTGGGATGTGGTGGTGTGACCCAGGTAGCTCCACGTAGGAAAGGGACTGCCCTGACAGTGCCTGCCACCTAGGGACAAAGCCAGCAGTGAGAGATGTCAGGGTCGGCAGGTCCCCTTTAGGTGCAGGCAGATGTCTTCCCATGTAGGTGCGTGCACCGGGCCCCTGGGAACAGCCTTCTCTGGGGCCTCCAGCCCTATGCGGTGGGCTTTCCAGGTGCACACACAGCTCCTTCCTCTTCACTAGGGCTGTTCTGCAATTGCTGGGTGTGGGCCGCTGCTGGGACACGGGCCTCCACTGGGACATGGGAGCCAATGCTAACTCTCAGCCTTATTCCCCCACCTGGCACCCTCCTGCCTCTAG
Seq C2 exon
TGGTGGTAACAAGCGGAAGCTGAGCACCGGCATCGCCCTGATCGGAGAGCCTGCTGTCATCTTCCTGGACGAGCCGTCCACTGGCATGGACCCCGTGGCCCGGCGCCTGCTTTGGGACACCGTGGCACGAGCCCGAGAGTCTGGCAAGGCCATCATCATCACCTCCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000167972-ABCA3:NM_001089:29
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:
PF0000522=ABC_tran=FE(42.8=100)
A:
NA
C2:
PF0000522=ABC_tran=PD(18.6=46.6)
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:
CAGCGGATCGGCTACTGC
R:
GTGGGAGGTGATGATGATGGC
Band lengths:
351-835
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)