GgaINT0013248 @ galGal4
Intron Retention
Gene
ENSGALG00000005315 | RPUSD1
Description
RNA pseudouridylate synthase domain containing 1 [Source:HGNC Symbol;Acc:HGNC:14173]
Coordinates
chr14:5983778-5985848:+
Coord C1 exon
chr14:5983778-5983879
Coord A exon
chr14:5983880-5984100
Coord C2 exon
chr14:5984101-5985848
Length
221 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGG
5' ss Score
6.92
3' ss Seq
TCCTGCTCCCCCCCTCCCAGGGC
3' ss Score
9.82
Exon sequences
Seq C1 exon
GCTGTGAAAACCCCAAGCCGTGCCAGTCGGAGCTGATTGTGCTCGAGCACGGGTCGTACAGCGGAGATCCTGTAACCAAAGTACTGCTGCAGCCGCTGACAG
Seq A exon
GTGGGGCTCTGGGGGGGCTCACGTGGTGCATGTGTCCATAGTGCAGGGTGGGATCTGTGCTTACAGCCCTGGGTATTGGTGGTGCAAAGCAGCCCAGGCGGGGCTGACTGAAGCTGAGCTCATGGACTTGAGTTCTCCAATTGGAGGGACGCCAATTAGAGGATGCCAAGGGGGGATTTGGTGATACCCTGTAGCCCCAGTTCCTGCTCCCCCCCTCCCAG
Seq C2 exon
GGCGCACCCATCAGCTCCGAGTTCACTGCAGTGCCATCGGCCACCCCATCGTGGGGGACTTTACGTACAGCCACAAGAAGGACAGCGGTCCATACCGCATGATGCTGCACGCCTACTACCTGCGCATCCCCACCAGCAAGGAGCTCATCGAGGTCTGCGCACCCGACCCCTTTGTCACAGCCCTGGATGGCAACTGGGTGCCGCAACGCGTTGTGCACCGCCTGGACGAGACCATCCAGGAGCTGAAGGACAAGGCAGTGCAGAAGGGGGACGTGGGGCAAAGCCAGCAAGCCATGCCTGGGGACAAAGGAGAGGAAGCACTGAGCAAAGCCAAGAGCCCAGAGCTGGAGGAGCAGCGTGTGCAGTGCGAGCAGTGGTTGGCCGAGTGGGCCCTGGAGTGAGCGCCGGCCATGTCCACACGTTCCCAACCCTTTGCTCCATAGTCGTCTGATGGGTTCTGGCAGCCTGCCCCCAGAGCCCAGCACCAACTCCACATCCACACTTTCCATAGGTTGTGGTTTCCCTCACCTCTGGGTCTGGGATTAGGCGGATTTTAGCAGCAATTAGGATCGGTTTCTTTTCTTACCGTGCCCATCACCCATCTGGCCACCGGATGCCCCTTTCCTAATTGTGTGCCACAGCAGCAGTCAGTGTGCCACGCACCAGCTTACAGTGACCCTGGAGCTTTGCATCCCTGTGCCGGGGCAGCACGGCTGTGCCATGAGCGTGCCGGATGCACCCACAGTCCCACAGCACTCGGGTGCTCAGTGTGCCCTCCGTGGGCTCCGTGCCCACTGCTCCATCCCACGGCGGTCCCCAGTGCAGGAGGTGAGATGTCCCCTCCTTGCTTACTGCCCATGAGCTGGGACTGCGGCACGGCTTCGCCACCCACCTACGTGTTTTTAAAGGTTTGTTGAAGATGAGCAAGTTGATATGAAGAGATTTTAAAGCTTTTTTTTTTTTTCAGATTTCTATGGAACGAATCTTGTCTTTTAGCAGTTCTGATGGTCCCAGAGATGCACGTATTTTTAGTACTTACCTTGTATTAAAGCAGCCAGCATCCCCACGCTTTTTCTAATAGATTCTCCTTTCTACTAGCATTCCCTTTTTTCCTGGGTGTGGAGGCAGCTCCTGCTGAGATGGATCGGAGGACAGATGGGGGGGTGGCGGGGGCTCTGGGGATCAGCAGGGCTGGCTCCTCCCCACCAGGGCCCATCCCCACCTCCAGGTGTGCCTGGGGAGGCCAGGCAGCTGCAGGCACTCCTGAAGCTGTAAATTAACAACACTGAGTGTTTGCCAAAGAATTAATGTCAGGGACGTGCCCGGGAGGGCCGAAAGGTTACGGGTCACATTTGCTGCATCAGAGCTGGGATGCGCCCATCCGTGCAGGAACATCCCCGTGCCAACGGTGGCTGCAGCCACACACTGGGGGACACCGTGCCGTCGACAGCAATGGCAGCATGGGGACACTGTGCCATGGGGGCAGTCACAGCCGGAGCACCGTGTCCCGCAATCCCGCACTGTGTTGCACTTTGAGTGATATCGGGAGCCAGCCTGAAAGCTATTGCTGCCCACATCACCTCCACGCAGCGTTCACTGCGTTTTGTGTAGATCCACTTTGTGCACGTGAAGCATGGAGGGAGTCATGTTTGGGTATATGTGTGTTTCGTGGTCTTCTGTACCCCTGGTAACAACCCTTATTTATTGCGTATTTGTGGGCATCGCCATAGTAAACCATCTCCTCCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005315:ENSGALT00000008518:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.241
Domain overlap (PFAM):
C1:
PF0084917=PseudoU_synth_2=FE(20.5=100)
A:
NA
C2:
PF0084917=PseudoU_synth_2=PD(6.6=8.2)
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:
ACAGCGGAGATCCTGTAACCA
R:
CACTGCCTTGTCCTTCAGCTC
Band lengths:
305-526
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]