DreINT0025679 @ danRer10
Intron Retention
Gene
ENSDARG00000007219 | actn1
Description
actinin, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-081113-4]
Coordinates
chr13:36209108-36209470:-
Coord C1 exon
chr13:36209362-36209470
Coord A exon
chr13:36209249-36209361
Coord C2 exon
chr13:36209108-36209248
Length
113 bp
Sequences
Splice sites
5' ss Seq
CAGGTGATA
5' ss Score
4.58
3' ss Seq
ACCACTGTGTCTTTCCTCAGAGA
3' ss Score
10.59
Exon sequences
Seq C1 exon
TGAGCTGGAGTATTACGACTCTCCCAGTGTAAATGCTCGCTGTCAGCGCATCTGTGATCAGTGGGATTCGCTGGGAGTGTTAACTCAGAAACGCAGTGAGGCCTTGCAG
Seq A exon
GTGATACAGCCCTTCATATTCCAGCATTAAATTCATTCTTTCTAAAAAGCGAATGGTCTTTTTTTTAAACGGCAGTGCACTCACGTGTGTCTCACCACTGTGTCTTTCCTCAG
Seq C2 exon
AGAACTGAGAAACTGTTGGAAACTATTGATCAGCTTTACCTGGAGTTCGCCAAAAGAGCAGCGCCCTTTAATAACTGGATGGAGGGAGCAATGGAGGACCTGCAGGACACTTTTATAGTCCACACCATTGAGGAAATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000007219:ENSDART00000140243:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(34.0=100)
A:
NA
C2:
PF0043516=Spectrin=PD(0.1=0.0),PF0043516=Spectrin=PU(32.1=76.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCTGGAGTATTACGACTCTCCC
R:
ATTTCCTCAATGGTGTGGACT
Band lengths:
244-357
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]