HsaINT0003161 @ hg19
Intron Retention
Gene
ENSG00000072110 | ACTN1
Description
actinin, alpha 1 [Source:HGNC Symbol;Acc:163]
Coordinates
chr14:69349590-69351025:-
Coord C1 exon
chr14:69350885-69351025
Coord A exon
chr14:69349773-69350884
Coord C2 exon
chr14:69349590-69349772
Length
1112 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
ATATTCCCATCTCTGTCCAGGGA
3' ss Score
8.78
Exon sequences
Seq C1 exon
CGGACCGAGAAACTGCTGGAGACCATTGACCAGCTGTACTTGGAGTATGCCAAGCGGGCTGCACCCTTCAACAACTGGATGGAGGGGGCCATGGAGGACCTGCAGGACACCTTCATTGTGCACACCATTGAGGAGATCCAG
Seq A exon
GTGAGCCCCACCTCCACTCCCCGGAGGCTGGCTCCCCTGGGGCCCCTGGCCCATGCTCTGTGGGTCACTTTTGCAGGACTGCCCCCTGAGGAAGAGCATCCTAAGGATTTTATAGACCCAGAACCTTTGCATTTGACTTATTTTGACAAGATAATATATGTGCATGATCTAAAATTTAAAAAAAATTAAAAAGGTTTATGATAGGGTCTCCCTCTGACTCCTTATCCTCCAGCCCCTAGTTCTCTCCCCAAAGGTAAGAATTTGACTACAGTCTCTGCACACAAGCAAATGTTTGTTTCCATGCTTTGTACCCTTTTTGTATAAAACAAAAAGTACCTTTTATTATATACCATATTCTGAACCTTGATTTTTATTTATTTTATTTTTTTAGAGACAAGGTCTCACTCTGTCACCCAGGCTGGAGTGCAGTGGTGGGATCATAGCTCACTACAGCCTCCAACTCCTGGGCTTAAGCGATCCTCCTGCTGCAGCCTCCCTAGTAGCTGGGACTACAGGCTCACATCACCATGCCTGGCTAATTTTTTAATTTTTATTTTTGTGGAAGTGGGGTTTTTTCTTTGTTGCTCAGGCTGGTCTCGAACTCCTGGCTTCAAGAGATCCTCCCATTTCGGCCTTCCAAAGTGCTGGGATTACAGGCATGAGTCACTGTGCTCAGCCATGAACCTTGATTTTTAATGTAACATTTATTTGGAGCTCATTTCACATCAATTAGCAGCTTCCTCAATCTTTCATGCAGTTGCAGAATACTGGATTTAAAAGGTTTTGCCAGGAGCTAAGGAAGCTCATGTTGTGGGAGGTCACCTGGGTAGTGAGCCTCTGGAGCAGCCCTTCTCCCTGACCTGTGAGGTGGTGAACACACCAGAGAGGTTGCTGCTAATTTGACCAGCCCTAAGGATGAAGCTGTTGCTTTTGATGACTGTGGCTTCACCTTCCTGTGGCCATACCTGCCATCCTGGTTCTCAGCCACAAGAATCTTTGAATTGATGCCTCCTGGTCTCCCAGCTGGTGTGGAACTCAACCTCCATGGCCCTTCCACTCACTTCTAGCGCTCCCTTTGTTCCTCTTGCCCACATATTCCCATCTCTGTCCAG
Seq C2 exon
GGACTGACCACAGCCCATGAGCAGTTCAAGGCCACCCTCCCTGATGCCGACAAGGAGCGCCTGGCCATCCTGGGCATCCACAATGAGGTGTCCAAGATTGTCCAGACCTACCACGTCAATATGGCGGGCACCAACCCCTACACAACCATCACGCCTCAGGAGATCAATGGCAAATGGGACCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000072110-ACTN1:NM_001130005:14
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.012 A=NA C2=0.199
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(0.1=0.0),PF0043516=Spectrin=PU(32.1=76.6)
A:
NA
C2:
PF0043516=Spectrin=FE(58.3=100),PF0043516=Spectrin=PU(0.1=0.0),PF088696=XisI=PU(2.4=3.3)
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:
GACCGAGAAACTGCTGGAGAC
R:
TGGTCCCATTTGCCATTGATCT
Band lengths:
321-1433
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)