GgaINT0057651 @ galGal4
Intron Retention
Gene
ENSGALG00000009474 | ACTN1
Description
alpha-actinin-1 [Source:RefSeq peptide;Acc:NP_989458]
Coordinates
chr5:27566823-27569007:+
Coord C1 exon
chr5:27566823-27566969
Coord A exon
chr5:27566970-27568926
Coord C2 exon
chr5:27568927-27569007
Length
1957 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
CTGGCACACCGCATAACCAGGAC
3' ss Score
2.91
Exon sequences
Seq C1 exon
CATATTCGTGTGGGCTGGGAGCAGCTATTAACAACAATTGCTAGAACCATTAATGAAGTGGAAAACCAGATTCTGACCCGTGATGCCAAAGGAATAAGCCAGGAACAGATGAATGAGTTCCGAGCCTCTTTCAACCATTTTGACAGG
Seq A exon
GTAAGTCAGTGTTGACTGCAGCTTGGTAAGCTGCAAGCTTCCATGTAGACTGCACAGTGCAATAAGAAACAGTTACCATGATAAAACTAGATCGATAGAATGTGTTAGATTCTTAAAAACACCACTCCTGTGGAGCATGGAGACTGAGAAGTGATCATTAGACTGAAGGATATCTGAAATGCAAAGATCTCTGGTAAAGATAAAGTTTGAAAATGTTTGAAGGCTTATTTAGGAAATCAGATTTTTAGCTCAGCTTCACTATCTTGATTTATAAAATCGTTCAGAGCAGCCATCCTCCACTCCAGTACACCACTACATAAACTGATACAGAAAAAAACAGCATTGCTCTTGTATGGAGCAAACAGGAGGACCTATGCGCAGCATGACACTGCAAAGCATAAATAAACACTGATGTAAAGCCTGCCTTGCCTTACTGTGGAAATACATGTAAAGGCACTAACAGATACAAAAAGAAAAGATTTTCTCAAAGAAAATCCTCCCCTTGGTTATACACGCTCCCTGCAGCTCTTTCTTCTATGGTGAGAACAGATAGCATCCTTCTATCGACCAAATCAGAAAGCTTTCACACAGGGAGGCAGAGACAGCAGCCCAAGCCTGACACCATCTCGTGACTGGCTGTAGGTTCAGTTGTTAACCCCCTCAGTGTTTGGAAATCCACGAGCAGCCTGCAGGTACTAAATCAGTGATGAAAATGTAGGTGGCCTCCACCATTTGCTGCACAATCCAGACTGTTTGAAAGATCTCCTGAGAGCAGGACTACAGCTTCCCCTCTCAGAGGCTGACAACACTTTCAGATTGCTGAGCACATTTGAGCCCCTCTCTAGCTTTTCAAAGGAAAACCAAAACCACGCCTTCCTTCCTTAGCAGGCCCCGGACAGCCCCGTAGATTTAACATTTTTACCTGTATGTCATTTGCCTTTTCCTCCACAGCAGTCTGAATGATAATGCAGAGAGATTGCATCTTTCCCAATCTTCAGCTATGTATTTGGGTTATGAGGGCTTTAAAAAGCTGACTGTTTAAGGAAAGTCACATGGAATTGGCCCCACAATGATGTTTGTAGCTTCCTTTCTATGGCTAGAGATGGTGGCTGCCAGCAGGGGCTCTTCAATGCCTGGGGCTGTCCTGAGCTAAAATTATGTGGGGTGAATGGGGATTCTCAGTTCATGTGGTAGTTTGTGATCATGGATACATCCAAACACTGGGAGAGCAGGGAATAAGCAAGGGAAGGAGCAGCTGCCAAGCCTCATTGTGCCGTGCTGTACAGTAGTGCTGTTTTCAGAGCTGAGCACTTCAAACAGCTTGCCAGTCAAAGTTCCACCTTACGTGCAGGTCTCATGAATACAGCAATAACACTGCTCCCTTGAGCTTCAGCTGTTTTTCTTTGTCTGTTCCTGGGATGCCCTGACAGCTCAGCTTCCTTGGGTGTGTTGCCAAACATACCTGCCCTCACCTACTCCTTTGGTGGGACTTTTGACTAAAAGAATAAGGCAATGCTTCCCACTGCCTCTTCCTGCTTACCTGCACTCCAGGTTACTAGCGAAACACAGGGCTTCTGGCACTACGGATAACAAGCAGTGATGCAAGTAATTCACTTGGGAGATAGAGATCTTAAGGCTTCTGAGCAATGACTGTTTTTGTCATTCAAACGCTCTCAAGATGTGATGAGCTTTCTCAGAAGGAACTGTTCCAAGAGCATTTTTAGCACATCCTGAAATGTCATTGTGATATCTAATGTTGTGCACTTTTTATTTTTCTTTCCTGTGTTTCTATCCGCATGTCATTCTTCCTCTCCCTGTCTTCTCACCCACTGCATGGTGCACCTGTTTGTTGTCTTTCCACCTCCGTTTGATTTCCTCTGTGTCTCCCTTCCTTCTGCTCCACACCGTCACCCCACTGGCACTGCATGTCCTGCTGCCTGGCACACCGCATAACCAG
Seq C2 exon
GACCACTCCGGCACACTTGGCCCTGAGGAATTCAAAGCCTGTCTCATCAGCTTGGGTTACGATATTGGAAACGATGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009474:ENSGALT00000038021:19
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(20.2=42.9),PF088696=XisI=PD(31.9=44.9),PF134991=EF-hand_7=PU(32.9=57.1)
A:
NA
C2:
PF134991=EF-hand_7=FE(30.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATATTCGTGTGGGCTGGGAG
R:
TGTGCATCGTTTCCAATATCGT
Band lengths:
227-2184
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]