GgaINT0093399 @ galGal3
Intron Retention
Gene
ENSGALG00000013073 | UPP1
Description
NA
Coordinates
chr2:82227742-82229396:+
Coord C1 exon
chr2:82227742-82227951
Coord A exon
chr2:82227952-82229249
Coord C2 exon
chr2:82229250-82229396
Length
1298 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
TCTACAAAATGGCTTTGCAGGAC
3' ss Score
6.22
Exon sequences
Seq C1 exon
GTCTGGAACCAGGCTCAGTGGTTATAACCAGGCAGTCTGTAGATGCCACCTTCAAACCTCAGTTTGAACAGGTTGTTCTGGGAAAAACTATAATTCGCAGCACAAATCTAGATGAAGAGCTGGCTAAAGAGCTGCTACAGTGCAGTAAAGAAATCAATCAGTTCAATACTGTCATTGGAAACACTATGTGCACTTTGGATTTTTATGAAG
Seq A exon
GTATGGCTGCAACAGACTAGCAGAAATATGGATTGACATACAGACATCAGGTGCTTCTCTGGTCTCTCATATCTGTTAACAAAATCTTTCAAATCTCATGAGAATGGGCTGAAGACAGCAACTAATGCTGCTTTCTCAAGCAATTGCTGGGTCTGTGACAAAGGGTGCAATGTGCAGGGGGGACTCTTCGTAGTCTTCCAGATGGGCCAGAAGCAGACAGTGTCAGCTTGTGCATCTCTTCAGACACCAATCGCAGAGCCAGGCTGCACTAAAAAAAAAGGAGTCAGGAACGTTCTCGATACAGACAGCAGGAGCTGAAAAGAGGCTCAAGGACATGAATTTCAGAATACACCTCCTGAAAAGAAATAGATAGTAAAGTACCATGTCATTTAATTATGCTGTATGTAATGTGCTGCCATTTTACCTGTAGATGTTAATCTCAAATAATCTGAATAAATTGTTATTTCCAAAGAATGGTATTGCACAGAATTAAGGGGGCTAGAAGGGACCTTTGGAGCTCACCTAGTCTAACCCCCTTGACAAAGCAGGTTCCCTACAGGAAAGTGTCCAAGTGGGTTTTGAATATTTTGAGAGAAGGAGACTCCACAAGCTCTCTGGGTAGACTGCTCCATGGCTCTGTCACCCTCACAGTAAAGATCAGATGGAACTTTCTGGGTTCCAGTTTGTGCCCGTTGTCCCTTGTTCTGTTGCTGGGCACTGCTGAAAAGTCCAGGCTGAACAATCCCAGCTCTCTCAGCCTTTCCTCATAAGAGAGATGCTCCACGCCCCTCATCATCCTTGTAGCCCTCCACTGCACTCTCTAGAATTTGCCTAAGAATTAGTATTAACTATTTAGCAGAAGAGACTCCCAATCTCTAAGCTTTTGAAGCTAGTATCAGGAGCTTATTTTCAGGCCTGGCAGTCTTTCTAGACAATGATTAAATACAGGAAAAAGTGCTGCACTTCCATACAGCTTAAAGCAGATGTAGTTTGCTGCAAAATTCTGACACGTGCCCCATGTGGGGAAAACCACTTGATATATTCCTCTGTTTATGAGTTTGAAAGTTTAAGCTGGAGAAGACCAGTAAAGTTATTGTGAGTCACATTATAAAGAATGCAAGTAATACATAGAAGCTCTAGCAATAACTGAGAGTCACTTTGTCTTCTTTGTCTTTGGGGATGCGGGAAAATGTTAGTAAAATGTAGACACTGTGTATGGGAAACTGTAATAAACGGGTATTTTAGAAATTTAACTTGATTTATGACTTCATCAGTATTTCTACAAAATGGCTTTGCAG
Seq C2 exon
GACAGGGCAGGTTGGATGGTGCAATCTGCTTGTATAATGAAGAAGAAAAACTGCAATATTTGAAGGAAGCTTACGATTCCGGTGTCAGAAACATTGAGATGGAATCTTCTGTCTTTGCTGCAATGTGCAATCTCAGTGGTGTCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013073:ENSGALT00000031003:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0104815=PNP_UDP_1=FE(27.9=100)
A:
NA
C2:
PF0104815=PNP_UDP_1=FE(19.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGGAACCAGGCTCAGTGG
R:
TGACACCACTGAGATTGCACA
Band lengths:
353-1651
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]