GgaINT0050746 @ galGal3
Intron Retention
Gene
ENSGALG00000012554 | UPP2
Description
NA
Coordinates
chr7:37941867-37942678:+
Coord C1 exon
chr7:37941867-37941981
Coord A exon
chr7:37941982-37942468
Coord C2 exon
chr7:37942469-37942678
Length
487 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGC
5' ss Score
7.96
3' ss Seq
CTCAGCCTCTGCTTTCCCAGGGG
3' ss Score
7.3
Exon sequences
Seq C1 exon
CACGGAATGGGCATCCCTTCTGTGTCCATCATGCTTCACGAGCTGATCAAACTGCTGCACCACGCCAAATGCCGAGACGTCACCATTATACGCATTGGTACTTCTGGAGGCTTAG
Seq A exon
GTGAGCTGTCCCAGCTCTTCCTTCCAGGCCAAAGGGTATTAACAGGTTTTTTTCAGCATAGTCATGTCATTATGAGCTTTTGATTTTGGCAGGTCCCCATGTATCAAATAACATGATACTTTATTCAAGGCTAAAACCCAGCACGATCCTGGTGACCAGCTTAGCAGAGCACGTTTTTGTTATGCCTGCTGGGGCAGCGGTGCTGCTCACACCTGCACGGCCTGGTGCCACGGCATGGCTCTGCATCCATCAGCAATCAAAGTGCTGTCACTCAGCACACCCCCAGTCATTCATCACGTGCTGGTTCTGTGCACTTTACTTATACATCTGTGCCACCACATAGCTTTCAATTATTCCCTCACATCTGCTTCGCTCACTAAAAACCCATCGCACAGATACCTGCAGGCATTTTTCTGTGGTGCTGAAGCCTTGCAGCAGATCACCAGCACCGTGAGCTCAGGCTTAGCCTCAGCCTCTGCTTTCCCAG
Seq C2 exon
GGGTGCAGGCCGGCTCCGTGGTGATCACAGACAGGGCGGTGGACGCCCGCTTCCAGCCACGGTTCGAGCAGGTGGTGCTGGGCGATGTGGTGGTGCGGGGCACCGACCTGGACGGGGGCCTTGTGGAGGAGCTGCTGGCTTGCAGTGAGGCCATTCCTGACTTCCCCACTCTCGTCGGGCACACCATGTGCACCTACGACTTCTATGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012554:ENSGALT00000020501:4
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(15.1=100)
A:
NA
C2:
PF0104815=PNP_UDP_1=FE(27.9=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:
CACGGAATGGGCATCCCTTC
R:
GAAGTCGTAGGTGCACATGGT
Band lengths:
318-805
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]