HsaINT0003159 @ hg19
Intron Retention
Gene
ENSG00000072110 | ACTN1
Description
actinin, alpha 1 [Source:HGNC Symbol;Acc:163]
Coordinates
chr14:69351492-69352292:-
Coord C1 exon
chr14:69352142-69352292
Coord A exon
chr14:69351601-69352141
Coord C2 exon
chr14:69351492-69351600
Length
541 bp
Sequences
Splice sites
5' ss Seq
CAAGTAGGT
5' ss Score
7.33
3' ss Seq
CTTGTCTCTTCCCTCCCCAGTGA
3' ss Score
11.17
Exon sequences
Seq C1 exon
GCAAAGAGGCCATGCTGCGACAGAAGGACTATGAGACCGCCACCCTCTCGGAGATCAAGGCCCTGCTCAAGAAGCATGAGGCCTTCGAGAGTGACCTGGCTGCCCACCAGGACCGTGTGGAGCAGATTGCCGCCATCGCACAGGAGCTCAA
Seq A exon
GTAGGTGGCCCCAGACACCCCTACCCTGTGGTGAGGGGCTGAGGCTGGGCTTTCTCAGCTGCTGGGGGAGGTGGGGGTGTGGCCGTGGAAGATGGGGAGGGTGGGTACAGGTGGGTGCCCAGGTGGGGAGGGAGTCAACGCAGGAGACAAATATCTCTCCTGGTGGGGAAGGAGCCCGGGACCACTGCCATCCTGTTAAAGGCCACCAGTTCTCGCCTGTAGCTAGTACAGGAGCAGAGGGTGACCAAGACTTGGTTCTGAGCTTTCTCGTTGGGCCTCGAGGGCTCCCTGCCATTGGCCATTGAGGTGAAGGCTGGTGTCACCTCCAGCCATGACTGGGAAAGGGGTCTTCTTTGGTCTCCTCTCTGCCAGTCTCCTGAAAGAGGGGAGGGGTGGAAGGAGTGCCTGGAAGGTCTCTTGAAGGGAGCGCCCCTGGCTCTTCCCAGCACCACCAGCCACCCCACTGACAGCCTCAGAGAGAGGGAGATGGGCCATGAAATTAACCTGGGTCCCCTGACTTCCTTGTCTCTTCCCTCCCCAG
Seq C2 exon
TGAGCTGGACTATTATGACTCACCCAGTGTCAACGCCCGTTGCCAAAAGATCTGTGACCAGTGGGACAATCTGGGGGCCCTAACTCAGAAGCGAAGGGAAGCTCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000072110-ACTN1:NM_001130005:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.010 A=NA C2=0.005
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(47.2=100)
A:
NA
C2:
PF0043516=Spectrin=FE(34.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAAGAGGCCATGCTGCGA
R:
CAGAGCTTCCCTTCGCTTCTG
Band lengths:
256-797
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)