GgaINT0093397 @ galGal3
Intron Retention
Gene
ENSGALG00000013073 | UPP1
Description
NA
Coordinates
chr2:82225654-82226976:+
Coord C1 exon
chr2:82225654-82225812
Coord A exon
chr2:82225813-82226861
Coord C2 exon
chr2:82226862-82226976
Length
1049 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGT
5' ss Score
8.46
3' ss Seq
AATTTCTGCTTTCATTTCAGCAC
3' ss Score
8.15
Exon sequences
Seq C1 exon
TTTGTGTGTGTAGGAGGAAGTCCTTCACGGATGAAAGCTTTTATTGCCTACATAGCTGAAGAACTTGGACTTGGGAGCTCTGGTGGTGACTACCCCAACATCTGTGCGGGAACTGACCGTTACGCCATGTACAAAGTGGGACCCGTTCTGTCAGTCAGT
Seq A exon
GTAAGTGACCTTTAGGAAACAGAACGTAAAAATGTCCATCCAGATACTACACATACATCAGATATTGAACATGATTCAGTGATGCTGTTCAAAGTAGAAAATCCGAAGCATGTTTTTTTTAAACACTTGATGGAGTCCAGTTTCTGTGTGTTTTCACCTGTGTTCAGAATAGTTCTATTGGCTAATTAAGAGTTTCTGTTTATCCCTTTCTTGTAAAAGGGCTGGTCCCCAAAACACTGATTCTTTTCTTGCCTTCTTTTCCCTCATTGTAACCCTGACGTGTTGCAAAGCCTTGTAAATGTTTTGAGCAGAATCACTGCTGTCTCATCCCTGCTTTTTATCCTGAATAATGGAATCATCACTTGATAAATGTGGGACACTGGAAAAAATGCATCTATTGCATATGCCTACAGTGGCATTTTCAAGTGTGCTACCATGGCTTATGATGGTCATTCCATGAGTGGTGGATGGAATCCACAGATTCCATGTGCCACCAACTCGTGTATGCGTTCTAAAAATTCACACCTTTAATTTGCAGATACAATTGCACACTTGAATTGCAATAACATAACTGTAATATCATTCTCACCCTTTCCCTTGACATCATCACGTAAGCTGAAGTGGACTTGCATTTGAACTTTGTGACTAAATAAACAATGGTTGTGTTTTAAAAAATTTTAGCTTAATTAGTCACTAGCTTTTCAGGTCAGTAAAAGGAGGTTTTTTACCCATGTTTAAGAAAAAATCCGTGGTGAAGTAAACTTATTGTAAACCTAGGAAAGGATGCTGATTTATACTTTCAAGAGCATAAATATTTTCTAAGTCAAGATTATTAGAAATACTGAACTTCATCCACAGTCCACAGATTCAATGGGAGTCCTTCTGTTTACTGTTCAAAAGTTTTTCAGTATTCCCATGAGTGTTTTCTGATGGTGAGTTACATGGCATTTGGAAAAAAGTATCAAGAAGGAGATAGTGCCTAACTCCTTCCATGTATATTTTTCACTGTCTATGTGAATGTCGAACATGAATTTCTGCTTTCATTTCAG
Seq C2 exon
CACGGTATGGGCATTCCTTCTATTTCAATCATGTTGCACGAGCTGATCAAACTGTTGTATCATGCCAAGTGTTCCAACATAACCATTATTCGCATTGGCACCTCGGGTGGAATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013073:ENSGALT00000031003:4
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(20.7=100)
A:
NA
C2:
PF0104815=PNP_UDP_1=FE(15.1=100)
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:
TTGTGTGTGTAGGAGGAAGTC
R:
CCGAGGTGCCAATGCGAATAA
Band lengths:
264-1313
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]