GgaINT0057650 @ galGal4
Intron Retention
Gene
ENSGALG00000009474 | ACTN1
Description
alpha-actinin-1 [Source:RefSeq peptide;Acc:NP_989458]
Coordinates
chr5:27565708-27566969:+
Coord C1 exon
chr5:27565708-27565887
Coord A exon
chr5:27565888-27566822
Coord C2 exon
chr5:27566823-27566969
Length
935 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAT
5' ss Score
8.39
3' ss Seq
TATTCTCTTTTTTTTTCCAGCAT
3' ss Score
9
Exon sequences
Seq C1 exon
GAGATTGGCCGCATTTCAATAGAGATGCACGGGACTCTGGAGGACCAGCTCAACCACTTGCGGCAGTATGAGAAAAGCATTGTGAATTACAAACCAAAGATCGACCAGTTGGAAGGAGACCACCAACAGATCCAGGAGGCGCTTATCTTTGACAACAAGCACACCAACTACACCATGGAG
Seq A exon
GTAAATGTTTTGCAGTGCCTTTTCCCTGCTGGAATGTACCACCAGCAGATCAGACAGCTTGATCTGTTGTTGCACCGGCCGCATCCAGTTCAGGCAATATGTTGTGGTTCTCAGGAAAGCAGAGAGCTTGACAGGATGGCCAAGCATGCAACATCATGTCACTGAATTTTTTTTCAGCCTTACTGTACTTTATGCCAACCCAGTCCGTTGTATTTCCACATACAACAATAGAAATAACCTAAATAAGATCAACGGTATTGCTTGAAAAAATTGGCTGGTCTTGTAGTCAGGCTGTGTTAGGCCACAAGCTGGAATTAGAAAGCCCAGACAAGAGTTGGTGATTTTCAGCTGCTATAGCATGGAAAAAGAAAAAAGTCCATCAGAACCTTTTCAAGATAAGAGTCTGGCTTTCTGTTGACAACATGAGGTTTCGTGGAAACAACCTGAATTCAGCATGAGTCCATCAGAACACAGACAGGCTTTGAAACTTGCTTTTTGGTTTCTGGCCAGCTCCGGCCATAGATGCAGTGGAGCACCAGTGTGTTCCAAGGATTGTGGTTCATTTGTTTTCTTTGTTCACGTAAAGAGTTTTCTGTCCAAATAAATCCTATAAGCATCAGTTTTGATTATCTTTTGTGTTAAAGGCTCCCACTGTGCTGAGCTACAAAGGAAAGGACCTTTGCAATAGGACCAGCACTTTATTATGAGCAGAAAGTGGCCTCTTCAATACTTTCTGCAGTCAAAATTCACATTTTAAACATCCAGTTGACTCATGCTGCGGATGAGAAAGAAGCTCTTCTAAGCATGCTTCTATGACTGCCTTGGCCATCAGGATCACTTAATTTGCCATAAGTGGCATGTTTGATCTAGCAGCCTCATAGGCAGAAGAGCTACTTTTTAATTTTAAAATTGTCTTATTCTCTTTTTTTTTCCAG
Seq C2 exon
CATATTCGTGTGGGCTGGGAGCAGCTATTAACAACAATTGCTAGAACCATTAATGAAGTGGAAAACCAGATTCTGACCCGTGATGCCAAAGGAATAAGCCAGGAACAGATGAATGAGTTCCGAGCCTCTTTCAACCATTTTGACAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009474:ENSGALT00000038021:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.039 A=NA C2=0.095
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(56.7=100),PF088696=XisI=PU(65.2=75.0)
A:
NA
C2:
PF0043516=Spectrin=PD(20.2=42.9),PF088696=XisI=PD(31.9=44.9),PF134991=EF-hand_7=PU(32.9=57.1)
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:
AGATTGGCCGCATTTCAATAGAGA
R:
AATGGTTGAAAGAGGCTCGGA
Band lengths:
318-1253
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]