GgaINT0057649 @ galGal4
Intron Retention
Gene
ENSGALG00000009474 | ACTN1
Description
alpha-actinin-1 [Source:RefSeq peptide;Acc:NP_989458]
Coordinates
chr5:27564736-27565887:+
Coord C1 exon
chr5:27564736-27564870
Coord A exon
chr5:27564871-27565707
Coord C2 exon
chr5:27565708-27565887
Length
837 bp
Sequences
Splice sites
5' ss Seq
GAGGTACAG
5' ss Score
6.62
3' ss Seq
CTTTGGCTTTGCTAACGCAGGAG
3' ss Score
4.92
Exon sequences
Seq C1 exon
GTGCGGCAGCTGGTTCCTAGAAGGGATCAAGCCCTAATGGAAGAACATGCTCGCCAGCAGCAAAATGAGCGACTTCGTAAGCAGTTTGGTGCACAAGCCAATGTCATTGGTCCCTGGATTCAGACCAAGATGGAG
Seq A exon
GTACAGCTTTTCTCATTTTCATTCTCTTCTCTGTGATCTTCGCTCATCCTTTTATTCTGATTCTCCTTTTACTACTGATGTGGTCATTATTCCTTGAGATTACAAGGGAAACTTCTATAGAAAATACAGAGAATCCAAAGATTAGTATCAGTTACCGAAGTGCTTGTACTTTTCTTCCCCTAACTTTAGTAAAGAGATAAAAAATGCTACCCAGAATGTGGAACACTGGTATTTTAATAGAGTTGAATTTATATGCAGCATGGGAAAGACCCTGCATCAAAAGCATATTTTATGGAACTGCTTTCATAGCAGTTGCACACGGCTCTTGTTACACATGAGAAAATAAATACATCTAGTGTGCTGAACATCAGCAGAAGAGAAACATTTCTAATGGAGATCTTCTCTCTTTAGGTAAACTATGAATTCAAGTAATTGGAGTTGGTAGGGTGAAAATGATGAAGCTGTTAATGAGGGTAGGAGATAAAAAGACAGCAATTAGAGAAATATTACTCTGCAGAAGCATTAACACAGTGGCAGAGAACGCATCAGGAAAAGTTCTGGCTTGCTACAGTACTAGCTTATGAACTACAGTTTCCTTCTTTTGCATCCTTATATTTGGTACATCTCATATGATGCACTCCACTTGGAAAATGTTCAAGGCTCTGCTGAAATTTCTGCTGACACTGTCTGCTCATCTGAAGTAACCTCTCTCTGAGATGTATTTTTGTTTTGATTCATCATCCCGTGTAAGCATGAAATAGCTGCATTAATAAATGTCAGCCATGTGAAGGCTCTTCCTTCTAACAGGGTCTAATACCTTTGGCTTTGCTAACGCAG
Seq C2 exon
GAGATTGGCCGCATTTCAATAGAGATGCACGGGACTCTGGAGGACCAGCTCAACCACTTGCGGCAGTATGAGAAAAGCATTGTGAATTACAAACCAAAGATCGACCAGTTGGAAGGAGACCACCAACAGATCCAGGAGGCGCTTATCTTTGACAACAAGCACACCAACTACACCATGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009474:ENSGALT00000038021:17
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(11.6=28.9),PF0043516=Spectrin=PU(20.2=46.7)
A:
NA
C2:
PF0043516=Spectrin=FE(56.7=100),PF088696=XisI=PU(65.2=75.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCAGCTGGTTCCTAGAAGGG
R:
TCCATGGTGTAGTTGGTGTGC
Band lengths:
310-1147
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]