GgaINT0124749 @ galGal3
Intron Retention
Gene
ENSGALG00000004689 | PKN3
Description
NA
Coordinates
chr17:5849937-5851759:+
Coord C1 exon
chr17:5849937-5850091
Coord A exon
chr17:5850092-5851629
Coord C2 exon
chr17:5851630-5851759
Length
1538 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
ACGTGCTTTGTGTTTGGCAGGAG
3' ss Score
8.02
Exon sequences
Seq C1 exon
ATGGATCTTTATCTCCTGACCCCTGTCTCTGGGAAAGAAACCCAGATCCCATGGCAAGGAAGATTGAAGCTCTGAAAAAGCAGCTGCATGTTGAAATGAAAGTCAAGCAAGGTGCTGAGAATATGATCCAGATGTATTCAAGTGCAACATCCAAG
Seq A exon
GTAAGCAGGAATAAACAACAATTTGGGCATATCGATTCCTGGAATTAAATACATATATATATTAAGTCCGTATACAAACTCTCTCTGGTAATTGGTGTGTGAAAGAAATTAATCTGTGAGGCATGCTTCCTAAACTGAATACTAGCTCTGCGTTTTGGTGCTCAGCATAGTGACAGCAGATTTTGATACTGCACGGGACAACCAATCGTATGAAAGTAACATGTTGCAGCAAGTCCAATGCATAGGTTGCAAGAATTGAAAAGGAATTGGATGGCGCATATATCATTTGTCAAGGGCTTAAGCTAATCTGTAATTACTGGATGTTAGGGCAAGGCTTTTCTGGAAGGGCATTTTAGTCTACTTTGGCCAATGGTATGGTTGCCTGTGCCTTTTATGAATCATGTGGTGATTACTGTTAGAGGAGAATTATTAGACTGGCCAGACTGGCACAGTCTGGCAATTTTGATCCTTATAGCAGTTCTTCCATGGCATTAATGATAGAGTTGGGAATCTTTTTTTTTTTTTTTTTTTTTTTTTTTTACCTCGGCCATCTAAATCCTTCTGTGAAAAGTTCTAGTTGAATAAACAGTTGCTGTAGGCACTCTCATTCATTCCTGAAGAGATGAATGACCTTTTGGAAAAACATTTCTTACACACTGCAGACTCTTCATGACTCCTTTGGTGTAGATGCTGAACTTGGCTGACTGAATGTCCACATAGATGTATTAAGACATCCAACCTCAATGTTCATAGCGACTTCAGTTTAGAGGCAGACTTGAGTTGGAGAGAAGTATCTCGTAGGAAGTGGCATGATAGAAGTGCTATCTCTAGAAAACGGAGATATTCTGTAATTCTCTTTAGCTTGAGAAGGTAGTGAGGGTAATATAAGAGGTACATTCAGTTGGTAATGTGAGGAAATTTAAGTTAAAAAGTGTTGTATTGTTCATTGAGTTGGTGTGATGTTTTGATACCACTGGGTAATTTAGGACGGAACTCAGCATGTAATATCTCTTTATTTGAGAGAAATTTTCAGTGCTTTACTAGTTTCATATTCATCCCACTTACTGAGTTTGGCATAATCATATTTGAAAGTCAAAGGATAATTTAAAAAAATCCAAGCTTAATTCAGTAAGACCAGCAGTGTACAGGGGTGTGCTATTCTGATATTCTCAAATGTTATGCTCAAAAATACTGTAGGTACAACTAACAAGTGAACGACAAGTCTCAGCTGACTGCCAGATTTGGTGTTAACTGACATATCTGTTAGGTGTTTTGTAGTAACTCATTTTTTTTCCCTTGGTGTCATAGACCATCAAAGACTCCTTGGGCTGTCCTTTCTCTCTAAAAATTGAGATAATGATCTTGAAGTCCTTGATCCTCAGCAATGTCTCTTTGACATAAATGCTTATGTATGCTATTTCAGAATTGTTTATATGATCCTTATTGCAGGTAGCATCTCACCCCTTAGCTGAACACATCACCATAATCCATTTTTAATGATCACGGTCCTTTCTCTGCACGTGCTTTGTGTTTGGCAG
Seq C2 exon
GAGCGGAAGCTGCTGGCTACAGCTAAGCAGATGCTTCAGGATAGTAAGACAAAGATTGAAATTATCCGCATGCACATTGTGAAGGTATCTCAGTCAGCAGGAGGGATGGACGATACAGTGGATCCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004689:ENSGALT00000007470:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.442 A=NA C2=0.205
Domain overlap (PFAM):
C1:
PF154561=Uds1=PU(50.6=76.9),PF0218511=HR1=PU(44.4=61.5)
A:
NA
C2:
PF154561=Uds1=PD(46.8=84.1),PF0218511=HR1=PD(52.8=86.4)
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:
TGGATCTTTATCTCCTGACCCCT
R:
GCTGGATCCACTGTATCGTCC
Band lengths:
282-1820
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]