HsaINT0003162 @ hg19
Intron Retention
Gene
ENSG00000072110 | ACTN1
Description
actinin, alpha 1 [Source:HGNC Symbol;Acc:163]
Coordinates
chr14:69349175-69349772:-
Coord C1 exon
chr14:69349590-69349772
Coord A exon
chr14:69349310-69349589
Coord C2 exon
chr14:69349175-69349309
Length
280 bp
Sequences
Splice sites
5' ss Seq
CACGTGAGT
5' ss Score
9.3
3' ss Seq
CCTTGTTGTTCCTGCCCCAGGTG
3' ss Score
9.49
Exon sequences
Seq C1 exon
GGACTGACCACAGCCCATGAGCAGTTCAAGGCCACCCTCCCTGATGCCGACAAGGAGCGCCTGGCCATCCTGGGCATCCACAATGAGGTGTCCAAGATTGTCCAGACCTACCACGTCAATATGGCGGGCACCAACCCCTACACAACCATCACGCCTCAGGAGATCAATGGCAAATGGGACCAC
Seq A exon
GTGAGTTGAAGGGCATGGGCCGAGCCATTGTAAGTTTCATAAAGGCAGGGATTTTTGTCCATTTTAATTGATTTTTGTCAATTTCATTTAAAATTGTCATATAGTAAACACTCATTGTTTGTCCAAATGTCAAATGACTGGGTTTCCAGAACAGGTTGACACCTTTACTCCTGTTCTGTTACTGACCGGCCCTTCCCCTTCTGGGTCCTCCATTTCCTCATCTGGCACATGGACAGATGGCTGACCCATCCTGAAAGTCGCCTTGTTGTTCCTGCCCCAG
Seq C2 exon
GTGCGGCAGCTGGTGCCTCGGAGGGACCAAGCTCTGACGGAGGAGCATGCCCGACAGCAGCACAATGAGAGGCTACGCAAGCAGTTTGGAGCCCAGGCCAATGTCATCGGGCCCTGGATCCAGACCAAGATGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000072110-ACTN1:NM_001130005:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.199 A=NA C2=0.264
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(58.3=100),PF0043516=Spectrin=PU(0.1=0.0),PF088696=XisI=PU(2.4=3.3)
A:
NA
C2:
PF0043516=Spectrin=PD(11.6=28.9),PF0043516=Spectrin=PU(20.2=46.7)
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:
ACAGCCCATGAGCAGTTCAAG
R:
ATCTTGGTCTGGATCCAGGGC
Band lengths:
305-585
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)