GgaINT0093398 @ galGal3
Intron Retention
Gene
ENSGALG00000013073 | UPP1
Description
NA
Coordinates
chr2:82226862-82227951:+
Coord C1 exon
chr2:82226862-82226976
Coord A exon
chr2:82226977-82227741
Coord C2 exon
chr2:82227742-82227951
Length
765 bp
Sequences
Splice sites
5' ss Seq
TAGGTATTT
5' ss Score
5.39
3' ss Seq
TTTGTTTCTTTCCATTGCAGGTC
3' ss Score
12.78
Exon sequences
Seq C1 exon
CACGGTATGGGCATTCCTTCTATTTCAATCATGTTGCACGAGCTGATCAAACTGTTGTATCATGCCAAGTGTTCCAACATAACCATTATTCGCATTGGCACCTCGGGTGGAATAG
Seq A exon
GTATTTCCCCTCTTGATTTCCTTTTTTCTTCAAACCAAAGCATCTCTTGTTGGAGAGCAAAGTATTTCTCCCCAAATGATTCATGTTCAGAACAGATTTCCACAGCAGATTATCTGAGTACATTTAATCATATCATGGAATCACAGAGCGGCTTGGGTTGGAAGGGACCTCAAAGCTCTCCCAGCCCCAACCCTGTGCCATGGGCAGGGCTGCCACCCAGCAGCTCAGGTTGCCCAGGGCCGCATCCAACCTGGCCCTGTGAGCCTCCAGGGATGGGGCACCACAGCTTCTCTGGGCAGCTGTGCCAGCACCCCAGTGAGTAAAAACAAAATTCCCCTAACATCTCTCTTTTAGTTTCAAACCATGATATTTCTTTTATTTCCTGGATCGTAATGTCCTTCCATTTCAAAACAATAAATAATTTTACAAGAAAAGGTGGTATCTGCCTCTCTAGATAGATAAAATGCACTTAAGAGATCTGACAGAGGGAGAAGGACATTCCTGTACTGTTTAAAATAGCAAAAATAAGAAAGAATATACGATGAAAAAGTCAAAATTTCATTTTTTTTTCCAGATATATTTGCAATAATAAACTGACGGGGTGAGGCATACACACACACACACAAAATCTCTTTGTGATTTTGGGGGTAAAATTATCACTTTCAAAAGAAACAGGGTTGGGTGAAGATGTGTGTTTTTTGTCTGTGGAAACTAAGCGTTACCTGCATCTGTTTCTGAAACTGCATTTGTTTCTTTCCATTGCAG
Seq C2 exon
GTCTGGAACCAGGCTCAGTGGTTATAACCAGGCAGTCTGTAGATGCCACCTTCAAACCTCAGTTTGAACAGGTTGTTCTGGGAAAAACTATAATTCGCAGCACAAATCTAGATGAAGAGCTGGCTAAAGAGCTGCTACAGTGCAGTAAAGAAATCAATCAGTTCAATACTGTCATTGGAAACACTATGTGCACTTTGGATTTTTATGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013073:ENSGALT00000031003:5
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(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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACGGTATGGGCATTCCTTCT
R:
AAAATCCAAAGTGCACATAGTGT
Band lengths:
318-1083
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]