DreINT0025694 @ danRer10
Intron Retention
Gene
ENSDARG00000007219 | actn1
Description
actinin, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-081113-4]
Coordinates
chr13:36212409-36213977:-
Coord C1 exon
chr13:36213885-36213977
Coord A exon
chr13:36212640-36213884
Coord C2 exon
chr13:36212409-36212639
Length
1245 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGC
5' ss Score
4.72
3' ss Seq
CTTGCTCTGGCTCTCTTCAGCTC
3' ss Score
9.22
Exon sequences
Seq C1 exon
GCCGAAACGGCAGCCAATCGGATCTGCAAAGTGCTGGCTGTCAATCAGGAGAACGAGCAGCTGATGGAGGACTATGAGAAACTAGCCAGTGAT
Seq A exon
GTGAGCACAGTCATTCATTCCTGTTCACTCCTCTTCACTCCCATCCTTCTCTCCTGTCGTCTCCTCGTCTGTGCTCATTTAGGGACAGTTTCAGTCATTTAAACTGCTTTCACAAGTACAGGAAGTTTTGTACTGCTGATGTTTAGGTCAAACAGTTCAATGGAATAATAATAAGTAAATGATTAATATATATGTATTCAATCGCTAATGGCACTTTGAATGTAAATGCAATTTAAATGTTAAATAAAATGTGTCTGAATAAATGTTCATTTTAGTTTTGTCATCTAAACTGATGACATTTCTTCTAAAGTTAAAATAAAAGTAGTTTTTAAAGCCTTTGGTATAAAATAATTGAAAACAAAATGTTTCATGTTAATTTCTAGACATCACGATTCATAGATTTTTCTTTAGAAATGTTAAGAAATCAATATTTGGTGGAAAACCCTGACAACAATCACAACATATGATGAAAGCGACTGTTATTCTGACTAAATTTTAAGTTAAATAAATAAATTTAAAAAATTACCTAAATTACTTTATTACTTTATATTACTTAATTATTATTTAAAATTTTTATTTAATTTTGTATTTTTGTTTTTACATTTTTAATAACATTTTGAAATGTGGAGGTGTTCTTATAGCATTTTTAATTTTTACTCAGTCCCATAACTTACAAATTCATTTTATTAGATCCATTTCATCTGTTTAGTTCCCCGTAAATGTATCTGTAATAATTCAATATATACTTTAATTACAAATACTTTAGTTGATCCAGGTTATTGACTGAAATTACACAATGACTCTAAAAGTCTTAAAATATTATGTAAATAATTTGGGTAACCTGTATATAGACCACTTCAATGTGGTCATGTCATTGGCCAGTGAAAATTTCCTGCTTGTTATCAAACTATTTTAAATCTGTAACAAGAGGCAATTCAATCATAACTTGATGTTACAACAGCTATCCTTACATTATTTATCAATATGTGGAACTATTTGGACTCTTAGAAGCTTTGGAAATGTAAAATTGAAAACAGGCAACGTCAGGACCATTGTTATTGTTTACATCCCTCAAAATGGTCTGTTATTCTTCATAAAACCATCAAAAGTTCTGATTCTCATTATCTCTTTTATCTCTATCTCCTTTATTTCATTCCGTCTGCTCCAAATTGATCCCTTTTCCCCCCCTCCTTTTGTTGTTTCCTTCCCCTTTTCCTGTCTCTGTCTTGCTCTGGCTCTCTTCAG
Seq C2 exon
CTCCTGGAGTGGATTCGCAGAACCATCCCGTGGTTGGAGAACCGCGTCCCAGAGAACACCATGCAGGCCATGCAGCAGAAGCTGGAGGATTTCCGGGACTACAGACGACTTCACAAACCACCCAAAGTTCAGGAAAAATGCCAGCTGGAGATCAACTTCAACACACTGCAGACCAAACTGCGTCTCAGCAACCGGCCAGCGTTCATGCCTTCGGAGGGAAAGATGGTCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000007219:ENSDART00000140243:9
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=PU(9.9=35.5)
A:
NA
C2:
PF0043516=Spectrin=FE(68.5=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:
GAAACGGCAGCCAATCGGATC
R:
CGAGACCATCTTTCCCTCCGA
Band lengths:
321-1566
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]