GgaINT0093400 @ galGal3
Intron Retention
Gene
ENSGALG00000013073 | UPP1
Description
NA
Coordinates
chr2:82229250-82230629:+
Coord C1 exon
chr2:82229250-82229396
Coord A exon
chr2:82229397-82230052
Coord C2 exon
chr2:82230053-82230629
Length
656 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAC
5' ss Score
7.2
3' ss Seq
ATATGTCTTTTCATTTCTAGCTG
3' ss Score
9.85
Exon sequences
Seq C1 exon
GACAGGGCAGGTTGGATGGTGCAATCTGCTTGTATAATGAAGAAGAAAAACTGCAATATTTGAAGGAAGCTTACGATTCCGGTGTCAGAAACATTGAGATGGAATCTTCTGTCTTTGCTGCAATGTGCAATCTCAGTGGTGTCAGAG
Seq A exon
GTAAACTAACTTAAAGTTGCTTTATTCAAGTAACAGAATGTTTTCTTCAGTGCAGGAGAATTCAGGTAAAAACTATCAATGGGGTACTGACATACCTTCTGCATAATATGCCATCTGCATGAAACAGCTCTGGTTGTAGGACTGTTACTATGATTGCTTGATTTGAGTCAAATGTATTCAAAATTTATGCAAACTTCTCATTGTTCTTGTATGCTTCAGTTCTGGTCAATTGCTATTCCAGCCGTTGGCAAGCACATAAGTCATAAAAGTATCTAATAACCCCTAGCACTGATTTGTTTTCCTCAGCTAAGTTTTGAAGTTTGCTGGAAGCAACTGGTTAATTTAATCAACCAGATGGTTTTAAAATGTATAGTGCTAAAATCACTGTCTAAACTTTTATCTCGATTTGAAAGCAGATTTTGTGTAGATGTACGGCTGTAACTTAAACAGTTACAGATTTTTGGCAGCATCATAGATCTTTCCTAATTATAAAGTGAGATTTAAATTATTTTTTACACAAGCTAACTAATTTTCAGTAAATTACAGGAAAAAAAATGAGCAACTGTAGTGTTCTTATGTTTGTTCAAATGTTCATGGCTTTAGACTGTCTGAGTACCAGAGTGCCATACCTAACTAATATGTCTTTTCATTTCTAG
Seq C2 exon
CTGCTGTAGTGTGTGTCACTCTCCTGAATCGGCTTGAAGGGGACCAGATCAGTAGCTCACATGATATACTTGTGGAGTATCAGCAGAGACCGCAGAAATTAGTGGGATATTTCATTAAGAAAAGTCTTGGGAAAGTATAACATGTCCATCTTTGGTTTTTAGAAGCAGAAGGCTTTTGCACAGCGGAAGTTGTGGTCACAACCTCTGTGCATTAAAGGTTTTTTTGCCTCAGAATAGCTTTCAGCATTCCATGTATATGCGGAAGTTAATCATTTATGTCAGTGTGCTTTGGGAACTGAATGTGCTGAATGCACTTCAGTTAAGATTAGTTTAGTTATTGTTGCTGGGATTTAAGATTCCCTTTTCTGAGTGGAAAGTAGTTCTGTTGTGAAGGACAAGCTTGCTGTGACGTTTGAAAAAGCTTTATTTATCCCTGCTGCTGAAGAAAAGGTAGGAAGAAGACAAAGTACTTTTTTGGGAAAGTACTTGCAAACCACCAAATTAAAATTAACTTAAGAATGATAATACCTTCCTTGTTGTTTTTTAAAAATATATAAAGTTATATAAATTATAACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013073:ENSGALT00000031003:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0104815=PNP_UDP_1=FE(19.5=100)
A:
NA
C2:
PF0104815=PNP_UDP_1=PD(15.5=83.0)
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:
TCTGTCTTTGCTGCAATGTGC
R:
AGCACATTCAGTTCCCAAAGCA
Band lengths:
346-1002
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]