GgaINT0057653 @ galGal4
Intron Retention
Gene
ENSGALG00000009474 | ACTN1
Description
alpha-actinin-1 [Source:RefSeq peptide;Acc:NP_989458]
Coordinates
chr5:27571072-27573995:+
Coord C1 exon
chr5:27571072-27571230
Coord A exon
chr5:27571231-27573109
Coord C2 exon
chr5:27573110-27573995
Length
1879 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CCCCTGTGTCTTCATTGCAGAAC
3' ss Score
11.2
Exon sequences
Seq C1 exon
GGAGAGGCAGAGTTTGCCCGCATCATGAGCATTGTCGATCCTAATCGCATGGGTGTAGTGACGTTCCAGGCCTTCATTGACTTCATGTCCCGGGAAACAGCAGATACAGATACTGCTGACCAGGTTATGGCTTCTTTCAAGATCCTGGCTGGAGATAAG
Seq A exon
GTGAGGCTCTATGGTCTTCCTTCCAATCTGTATTGTTCCTGCCTCCCTTTTTCTGTCTGCAGGAGGAATTGTCGAGAGAAGCACTCTCTAGCAAGGAGGGCATTTTCACGGGAACACTGCAGTGCTGGAGGAGTGCAAGGCTAAAGTGTGGGTTAATGAGCAGCTTGCCAAGGCACTTGAAAGTCCTGTTCAGCTGTCAGCAGATCAGCAGAACTATGCTGCCCACTCTTGCATTAAAAAATTAAGAGCTTAGTTTCAATTTGTTACTTTAAAATGTATGAATAGATTAAACAGATGGTTCTTGATTAATCTTCTTGAAAAACTGTTAATTACTGACAGCTATAAACTTGAAACAATCTTTGTAGATATACGTGTGGCACTGCAGTCATTATACAATCAATCACAGAATACTACACATGATCCTAGCCAAAAGGCCGAGCGGAGAGACTAGATTGTCATTAAAGATACGCTGTATCTGCAAGCTATACAATTTTAGAAGGGCATATTTTAATAATAAATCAGTTGAAAATAAGAAAAATCACAGGCTGATGCTGACTCTTCTAAATTTGCAACGTCAGTGGAACCAGATGATATAAAAAATTATATATTCTTAATTTTCTTACATAAAAATCCCCACTAATCTTCAATGTAATTAAAAAAATAGGTGATATCTCTAGTACTAATGATTCTTTGTGTTTTCTAATGATTTTATTCATCTCAAGTGAGACACGGGATTCTATTTCTCAGGCTATAATGAGTTATGCTTTCATCCAGCATTGGTTTCTGCGCTTCACTAATCATCTTTTCACAACCTGTAACGTAGAAACCCATGATGTCCATCTTTCTGTAAGGCATAATACCTGACTAAAGCCAGTTCTATTGTCTTTCAAGACCTGAAAATTCCAGCTTATCGTGATGGACTAAACACTGAGAAAGGAAGCTATTGGGGATATAGTGTTATTTACTAACTTGTTTATTCTTTACAGTACATTAAATATAATTGTCGGTGTCTAATATGCTGTAGTGACTATAACATGAATCAGACAGTATTTCATTACGAAGAAAAATCTCCTAGTCCTTCCAGTCACAAAATTGAAGGCATGAAAAAAGGAATAGAAAGGAAAAGGAAAGAGAGAGGGAGAGATACTCTGAAACCTGAGCTGTTATTCAGAAAACTGCAAGTGAGTCAGTTAGCTGAACACAATCAACTGGTTAGCAAACAGACAGTTACTGTTACTAGCTGCATGAAAAGAACCCAAGGTAGCCTCACCTTAGCCGAATGAATCTCCAGAAGCCGAATTTATGTAAGACATTTTGCTTCCTTATTAAAAATGTCTGCCGTGAAAGACAGGAATTATTAGCAGAGCTGTGAAAGCTTCCAGAAGCGTTCACTTGTCTGCTGCCTGCGGCGGTGCCACCAGCCAGGGCTATTGGGGCTGGCTCCTTTCCATGCTCTGAGGAGAGGGAATGGCAGCTCCCAAGCAGCACAAACTGCTGCCAGCCAGGGGCAGGATCCAAATGAAATTTCTGCTTCTTCCTGTTTGCCTTAAGCCGGACCTCCACTTTCAATGAGGAGGTACAACAATTTCTCTGAACTCCCACCAGGTCTATTCTTTAGGTGTGCCAGCATGTCTCCCGCAAAAACAATCCTCCTCTCCTCTGTAAAAACATTTTCTTGGCCAAACAGTAGGGAGAGCAACTGCGTTTCCCTGACAGGTGTGTGCCCAGTGAGATCTGTGTATGGGCACACGGTACAAGTCACATTGTGGTCAGCCCCTGGCTGCCGTCTGCTGCCCTGTGGGGGCAGGGAGTGGGGTCCCTCTGATGGACGTCGGTATTTTGAAGATAACGTCTGCCTTCCCCTGTGTCTTCATTGCAG
Seq C2 exon
AACTACATCACTGTGGATGAGTTACGGCGGGAGCTGCCTCCTGATCAGGCTGAGTACTGCATTGCTAGAATGGCACCCTACAATGGCCGTGATGCTGTACCCGGTGCCCTGGACTACATGTCGTTCTCCACGGCGCTCTATGGCGAAAGTGACCTTTAACTTTTTTCTGTCCCACCACGCAACCCTCCCCTCTCCCCGTCCAACACACCCTTCTTTCTCTTTGCAAAGCAGCCTCTGCTCCGCTCTTTTTTGTGTTTCCCTGTTTTGCTTCAGATAACAGATCACGTTTTTAAATGGGGGGAGGACATTGACATGACACCGCCTACCTTGCCCTTGAAATGACAGTTTACAAAATTATTTTGTGCAAAAAAAGTTACGTTTTAAAAAGAACAGACATATTTTATTATAGAAAAGGGTATTTTTCTCCACCAGATTGAAACTTAAAAAGAAAATGTTCCAATATTGCACCAAATATTTTTTGTTGTGACATAGAAAGTCGAGCACAATGTTACATTCCATCCTTTCCAAAAAGAACCAACCACCAACAAAACGCCACTTGTTCTGTTACCTTCTACATTTGCGTATGTCTCTTTATCACGTTTATCTTTGGAGGGGGGGAAGGCACACAAGTGCATGTGTTTGCTGGTTCACTCATTTCATGAAAATATTTTATGATAAACTTTTGAAATCGCTGTGTTTTCTAGGGAAAAAATAATGTACACAGCTCATGTTTTCATATTTAATTAAAAAATACAATATGCCTCCTATGTTTATCAGTGCACAACATTTTTTGTTGCTGAGAGTTGTCTGGTTTCAGATGAAGCTTGAGAGTTGATAACTTTGATATTGCTTGTCACAGACCATATTAAAAATTTCTTGTGATAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009474:ENSGALT00000038021:21
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=0.038
Domain overlap (PFAM):
C1:
PF134991=EF-hand_7=PD(32.9=52.8),PF087265=EFhand_Ca_insen=PU(26.9=34.0)
A:
NA
C2:
PF087265=EFhand_Ca_insen=PD(70.1=88.7)
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:
CCGCATCATGAGCATTGTCGA
R:
AAAGAAGGGTGTGTTGGACGG
Band lengths:
358-2237
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]