GgaINT0050747 @ galGal3
Intron Retention
Gene
ENSGALG00000012554 | UPP2
Description
NA
Coordinates
chr7:37942469-37944179:+
Coord C1 exon
chr7:37942469-37942678
Coord A exon
chr7:37942679-37944032
Coord C2 exon
chr7:37944033-37944179
Length
1354 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TGGTTCTGTTTCCTTTCAAGGTC
3' ss Score
10.84
Exon sequences
Seq C1 exon
GGGTGCAGGCCGGCTCCGTGGTGATCACAGACAGGGCGGTGGACGCCCGCTTCCAGCCACGGTTCGAGCAGGTGGTGCTGGGCGATGTGGTGGTGCGGGGCACCGACCTGGACGGGGGCCTTGTGGAGGAGCTGCTGGCTTGCAGTGAGGCCATTCCTGACTTCCCCACTCTCGTCGGGCACACCATGTGCACCTACGACTTCTATGAAG
Seq A exon
GTAAGACGTGCTTTGGCTGTCCTTTCCCACGCGGTGCTCTTACGTAGGCAGAGCTATCGGTGCCGCCGGTCCTGCGGGCTGCAGCTGTCCCACCGGTGTGTCAGGGTCAGTTCAGAGCAGTCTGCGCCTCCAGAACGTGCAATACAAATCCCAGCACTTAGCCAGGCCACGAGTTCTTCTGCTGATGGCACGTGTATGCACCTGGCACCCCATTAATGTTCGTAGTGCCACCTGTATGGCCGGCACTGCTGTAGGTGGTGGTGGAGCAGAAGGGGGAGCCATCCAGTAGCTGCTGCCCGGCCCAGCTGTGGCATGGCAGTGTGGGTGGTTGGGGACCCCAGCTGTGGGGGTCGATGGCCTCAGGCTCCAGAGAAGCAGCCCCGGTCCACAGCCCATCCGTGCAGATGAGTCATGCCCTGCTGCTCAGGACAGGACTGTAAGTTCATGTTAGCCAAACACCAGAAGAATGTCAGGAAGCGTGTGACATTTGGGCAAACAAGCTCCGGTTACTCTGGAACTGTTTTCTTTTCAAAACAAAGTGCTGATTACAGAGTAGATGAAATGTAATAAATGAAGAATTAATTGACTGAGAACTATCTATAAATCTCTGCTTGTGAATGCAACCATCTGTGCCTTCCTCAAGGCCACATTTTATTTAAATAGAAATTCATTAAGAGGATCAACGGTAGGAACAGCAATAAGACGCACAGGTTGGCACAGCCACAGGTTGTGCTCACCCAGAGGAGGCTGCACGAGGTGCAGGGCTGCAGGGCAGGTGTGGGGAGAGGACCCCAGGGCTGGGGGGTACCACGTGTGGTGGGTACCACGGGACCGCTGGGGCTGACGAAAGCCCACAGGGAGCAGCACAGGGAGCAGTGCCTCTGAAGCCAGGAATGCCGCGTGCAAAGAGCTCCCACTGCCTGCTGCCAGAGTCAGTCCCTAAAAGAACTAAACCTGAGTTGACGGGGCTTTCCTCTCCCTGATGTTCTGCACAGCTTGCTGTGCCTCTCCCACAGTGACTGGGTGTTGTTTGGATTTAACCTGGCATGCCTCCACCCGATGTACATCACAGGCCTCGGAGGGGCTGCGGCCGTTTCCCCCAGCAGAGTGCCAGATGCCTCCTGCTCGGCGGCCGGGTCTTCCTTTCTACAGTGTAAACCTACACTGATTTGTTTCTTGTACACAGAAACAGACTATGCTGGCCTTACAAGTTCAGGTTAACTGGGGCATGGGTGAGGTAACTGCAAAAAGAAAACTCGGTCAGCTCCAGCCAAAACATCGGCACTGCAGACAGCCGGGTCACTGTGTCTGCCGCCTGTGAGGGCAAGCAGTGATGGTTCTGTTTCCTTTCAAG
Seq C2 exon
GTCAAGGGAGGTTAGATGGAGCTCTGTGCTCTTTCTCCAATGAAAAGAAGTTGCAGTACTTAAAGCGAGCTCATGATGCCGGCGTGAGAAATATTGAAATGGAGTCAACGGCGTTCGCTGCGCTGTGCGGGCTGTGCGGGCTGCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012554:ENSGALT00000020501:5
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:
CCGGCTCCGTGGTGATCA
R:
CGAACGCCGTTGACTCCATTT
Band lengths:
318-1672
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]