DreINT0025680 @ danRer10
Intron Retention
Gene
ENSDARG00000007219 | actn1
Description
actinin, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-081113-4]
Coordinates
chr13:36207598-36209248:-
Coord C1 exon
chr13:36209108-36209248
Coord A exon
chr13:36207781-36209107
Coord C2 exon
chr13:36207598-36207780
Length
1327 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCTG
5' ss Score
4.87
3' ss Seq
TGTCTGTGTGTGTGTTGCAGGGT
3' ss Score
11.63
Exon sequences
Seq C1 exon
AGAACTGAGAAACTGTTGGAAACTATTGATCAGCTTTACCTGGAGTTCGCCAAAAGAGCAGCGCCCTTTAATAACTGGATGGAGGGAGCAATGGAGGACCTGCAGGACACTTTTATAGTCCACACCATTGAGGAAATACAG
Seq A exon
GTGCTGTACACTTGTCTGTCTGTCTGCCTGTCTGTGTATCATCTGTCTGTCAATCTGTCTAGCATCTATTTGTCTTACTGTCTGTGTATCTATCATCTGTCTGGCTGTCTATCAACTGTTTGTCTGTTTGTCTTACTGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATTTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCCGTCCGTCCGTCCGTCTGTCTGTCTGTCCGTCCGTCCGTCCGTCCGTCCGTCCGTCCGTCCATATCCATCCATATCCATCCATCCATCCATCCATCCACCAATCCATCCACCTACAGTGTCTGTCTGTCTGTCTGTCTGTTTGTCTGTCTGTCTATCTATATATAAATTTTGAAAATGTGCATAAAATACATGCTAAAATGATAAAAATGTGTGTTAATAGACAGAAAAACCATGTTGTTTTGGTCATTCTAAAACGCCTCAACCGTTTCAGTATTAGTGTTATGATATTATTAATGACCTCCAGAACTGTCAAGAGCATCTGTGCTTCATGTCTCATGGCCTCAAACGCCCCCAGGCGTTCATTGTGTTTCGGCAACGTCTTCTGAGGTTAAAGTCATATACTAAATAAAAAAAGATTCATGCAGCTTCTTCAACTGCAGCAAATTCTGTTTTCACTGTTGATTTTTAGGCACCACACAATCAGGAAGTGACTATTTTATTCTTTTTGACCCCATAATCTATCCTTACGTTAGCTTCTTTATTATGGTCTGTCTGTCTAATCTGGAAAAGTAAATCATTTATTTGGGTTCAATTATACATTTTGTGATACTTGTGAGATATATTTCAATTACACATTTCATTTTTATGAACATATTTTAATCGTTACAATGTATGTAAAACATTAAAAGGTTTAAACCAAAAACCTTACTAATTTAACATTTGAACAGAATTATCTCTTTGGTCTACCCATGCGTCCATCCTTCCATCCATCTGGTAGATTTCAAATGTGACTGTAAAGTGTGACGGTGCATTTCACAGAAAACTTAATGTCAGATGGAAAATGTAAAAGTTACTGAGGCAGATAATGTTTTATAAAGTTATAACACATCTCCTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCTGTGTGTGTGTTGCAG
Seq C2 exon
GGTCTCAGCACAGCCCATGAGCAGTTTAAAGCCACACTGCCTGAGGCAGATAAGGAGCGACAGGCCATCCTGGGCATCCATAATGAAATTGCTAAAATTGTGCAGACATACCACGTCAACATGGCTGGCCAAAACCCCTACACCACCATCAACCCCCAGGAGATCAATGCCAAGTGGGATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000007219:ENSDART00000140243:14
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=PD(0.1=0.0),PF0043516=Spectrin=PU(32.1=76.6)
A:
NA
C2:
PF0043516=Spectrin=FE(53.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAACTGAGAAACTGTTGGAAACT
R:
TCCCACTTGGCATTGATCTCC
Band lengths:
320-1647
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]