HsaINT0000672 @ hg19
Intron Retention
Gene
ENSG00000198691 | ABCA4
Description
ATP-binding cassette, sub-family A (ABC1), member 4 [Source:HGNC Symbol;Acc:34]
Coordinates
chr1:94508317-94509031:-
Coord C1 exon
chr1:94508892-94509031
Coord A exon
chr1:94508455-94508891
Coord C2 exon
chr1:94508317-94508454
Length
437 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCTC
5' ss Score
3.6
3' ss Seq
CGTCCTTCTTGTGCCTCCAGGTG
3' ss Score
12.38
Exon sequences
Seq C1 exon
CCTCACGGTGGCTGAGCACATGCTGTTCTATGCCCAGCTGAAAGGAAAGTCCCAGGAGGAGGCCCAGCTGGAGATGGAAGCCATGTTGGAGGACACAGGCCTCCACCACAAGCGGAATGAAGAGGCTCAGGACCTATCAG
Seq A exon
GTGCTCAGAGCTGGATGGAGACAGGGCCACAGATGGCAAATCCATGGCTCCCCAGTGCACCCAGGAGGCAGGGGAGGCTTGGAGCAGGAGAGCTTCTAAGGGTGGGAACACCTCTGTGAAGTTACACCAAAAATCTAAGAGCAGCCCCCAGATCATTTTCCCTGCAGAGCACTGTCTCACAGCAGCCTGGGTTTTATTTGTCCTGAGATTGATGTGCTTGAACAGTCTTCAAAGGGTCTGATCCGAGGAGGTGAGGGTTGCCCTTTCTGCATTTACAAAGCCTGAACAGTATTAGGGCTTTGAACGCTATAAACATCTAAGAGGCAGCACCAAACCACTGCTGGGTTAAGGTACCCCCACAATGCCACTTGCCCTGGGCCTTTCTCTTCCTCACCCTCCACAGCCCCTTAACTCTCCCGTCCTTCTTGTGCCTCCAG
Seq C2 exon
GTGGCATGCAGAGAAAGCTGTCGGTTGCCATTGCCTTTGTGGGAGATGCCAAGGTGGTGATTCTGGACGAACCCACCTCTGGGGTGGACCCTTACTCGAGACGCTCAATCTGGGATCTGCTCCTGAAGTATCGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198691-ABCA4:NM_000350:21
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.500 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=FE(32.4=100)
A:
NA
C2:
PF0000522=ABC_tran=PD(17.9=55.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCACGGTGGCTGAGCA
R:
CTGAGCGATACTTCAGGAGCA
Band lengths:
278-715
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)