HsaINT0003163 @ hg19
Intron Retention
Gene
ENSG00000072110 | ACTN1
Description
actinin, alpha 1 [Source:HGNC Symbol;Acc:163]
Coordinates
chr14:69347527-69349309:-
Coord C1 exon
chr14:69349175-69349309
Coord A exon
chr14:69347707-69349174
Coord C2 exon
chr14:69347527-69347706
Length
1468 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGT
5' ss Score
7.07
3' ss Seq
GCTTCCTTCCCGGTGAGCAGGAG
3' ss Score
3.09
Exon sequences
Seq C1 exon
GTGCGGCAGCTGGTGCCTCGGAGGGACCAAGCTCTGACGGAGGAGCATGCCCGACAGCAGCACAATGAGAGGCTACGCAAGCAGTTTGGAGCCCAGGCCAATGTCATCGGGCCCTGGATCCAGACCAAGATGGAG
Seq A exon
GTGGGTCCCATGCTGGGAAGCAGTGCTGGGGCTCCCACCCCTCCCCCCCGACACTATCCTAGCCAGCCAGGCTGCCTGTCTCCCTGGGTGGGACCCATGGAGGACTGAGGCCCGGAGCCCACCGTGGGTCTGCTGTTCTGTAGAAGGCTATGGGGGCCTATGTGAAGAAGCCCTGCTGGCAGTATCTGATTTGGGAGCAAAGACATATGAGGACACCACTAAGAAGCTGCCTGTGGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGTGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATCAGCCGGGTGTGATGATGCGTGCCTATAATCCCAGCTACTTGGGAGCCTGAGGCAGGAGAATCGCTTGAACCCGGGAGACGGAGATTGCAGTGAGCTGAGATTACGCCATTGCACTGCAGCTTGGGCAACAGAGCAAGACTCTGTCAAAAAAAAAAAAAAAAAAAGAAGCTGCCTATGAAAGTCCCATACTAGGGTCAGTTCCTGAGCGCCCGATCCAGCTTAATCCCCTTGATGTCTCTTGTTGATCAGGCCTCCCCTTCCTCTCCTCCTCCTCCTGAGCAATGAGCCTGGCCAAAGAAAATGATTGATCTTCCCAGAAAGAGAACTGAACCCCAGTAGAGCATAGAATTTTTTTCTGAATTGTGTGGGGTAGATAGTGGGGTGCTTTAGCAGATCAGGAAAGAGGCCCTGCTTGGCTAGAGCATGGCCTCTGAGTTCCTTAAGAACAGAGACCATGTTGAGTTCACATTGGTATGTGTCGCTCCCCTGCACCCCTGCCAGCACATTGTCCTTAGTAGACAGGCAGGAAATATCTACTGAATTGAACTGAGTGGACAGAAAGTGCTTTCACAAACAATGGTTGTTTACATGGATGAATAACAGACAGAAATGGGCATTAGGCCTGGCCTGCAGGGATGAATGGGATTCAGGTGGGCCAGGGCAGGCATCCCAGGAGGCGGAACAGCAGGAGCAAGAGCATGGGTACTGAGGAGGTGAGTGAGGTCTGCCGAGGCTACGAGGATCCTGGTTCAGTGGGTCCCTGAGATGGACAAGACTTGGGAAAGGGCATTTGAATGGCAAGCAGAGGAGTGAATATTTAGGTTAGAACTGACCCTGCATCCCCTTTCTGAGGCTGACAGGTACCCGAGAGTTGGTAGGTATTTCATCCAATGATAACAGTGCTTGTTATATACCTCTGTGGTGCTGTTTCCATACCTAAGAGCACCCATGCTAAAAGTGTCTTACTAATTACCAGTGATGGCCTCCTTAGGGCTGGGATGGGAACTGAGAATCATTTGAGGGCTTAATAAGTGATTTTGGAGGCCCCAGTCCCCACCCTATGGGAGCAGAGTGAGGTGGTCTGACAAGGTGCTTCCTTCCCGGTGAGCAG
Seq C2 exon
GAGATCGGGAGGATCTCCATTGAGATGCATGGGACCCTGGAGGACCAGCTCAGCCACCTGCGGCAGTATGAGAAGAGCATCGTCAACTACAAGCCAAAGATTGATCAGCTGGAGGGCGACCACCAGCTCATCCAGGAGGCGCTCATCTTCGACAACAAGCACACCAACTACACCATGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000072110-ACTN1:NM_001130005:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.444 A=NA C2=0.017
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(11.6=28.9),PF0043516=Spectrin=PU(20.2=46.7)
A:
NA
C2:
PF0043516=Spectrin=PD(3.9=9.1),PF0043516=Spectrin=FE(64.2=100),PF088696=XisI=FE(51.2=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:
TGCCTCGGAGGGACCAAG
R:
CTCCATGGTGTAGTTGGTGTGC
Band lengths:
302-1770
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)