GgaINT0047235 @ galGal3
Intron Retention
Gene
ENSGALG00000012561 | PKP4
Description
NA
Coordinates
chr7:38050371-38051847:+
Coord C1 exon
chr7:38050371-38050587
Coord A exon
chr7:38050588-38051714
Coord C2 exon
chr7:38051715-38051847
Length
1127 bp
Sequences
Splice sites
5' ss Seq
CAGGCAAGT
5' ss Score
3.1
3' ss Seq
AATGTGTTCGTCCAACGAAGGGA
3' ss Score
4.23
Exon sequences
Seq C1 exon
GAGTTGGAAATCTGCAAAGATCATCCAGTCAGCGTAGCACACTCACATACCAAAGAAATAATTATGCTCTGAACACAACTGCTACCTATGCGGAACCCTACAGGTCAATGCAGTACCGACTGTCAGAGTCTGGCTATAACAGGCTGCAGCACACAGCGCCCGCTGATGATGGGACCACGCGATCTCCATCCATAGATAGCATCCAAAAGGACCCCAG
Seq A exon
GCAAGTCCACTTGTGCTTTCAAGAACCAAACATACTTGTCATAAGATGATATTTACTGTCTTTATGAGAGAAGTCTTCGTATCATTGCTGTGAGGGTGATCATGCTCTGGAGCAGATGGAGGTGGCCCATGGCCTGCACTCGTCAGTGTTTAAGATGCATTTAGGCATCGCCCTTGGTAACACGCTGCTAATTTTTGGTTAGCTAAAAGTGATCAGGCAGTTGGGCTAGATAACCAGTGAAGGTCCCCTTCAGATGCATTACTCTTTTCTATTGTTGTTAGGGAGAAATAAATCTCCAAGTAGCGACTCAAACAAGATCGGTAACCAAACTTTCCTTTTCTGATGAGTGGATTCTGGGGACACCTGACTGGCCAGGCTGCATTAGCCTTTGAATAGCTATTCAAGTACTCTTCTTAGAACATCACTTCCTTAGGTTTTTGAAAATAGAAAAGCTTTGCTACTACTACTTCTTTTTTTCTTAACCATTCCTTTACAAAACGAAGAAAATGGCCCAACAAATGTTAATGGTAATTTTCTAAATGTGGGAGTTGGGCATAAGTATGCTTAATGACTTTTCCAGGATTTGGCTACGCAAAAGTGCTGTGTTTAATACAGTTTGATTACAATTATTTCAAATTCAGTATCCCTGATGAACTCAAATTTTTCAAATTTACGGCATCTGATGGTGGAATCTTGAGATTGCACAGCTTTTGTTCAAGTACAGTTGGCTTCAAATAAGAACGCTGACTGTGGAGAAAAAGATATTGCATAGAAGATAAATACTTAAGTGGCAATGTTCAGTGTGCATCTTGCATTATATATTTCAGCTTACAGAGGCTTATATAGGTTGCACTGTTTTAGCTGGTATAGTTTTAATAGGGGTATCTGTGTCGTCAACTACCAAACTAATGCGGGAGCACAGAAAATGAAGGGTCCTGTTCCAGTAAGAAGACTAGAAGCTGATGTGACATAGTTATTCTAATGGAAACGGTTTTCCTCCTAGCCCCAGTGCTCCAGAATGAAAACAAACTGTTGTGCAATACTTAAGATACTCTACTAGTTCTACTCAGTAAATAAACATACATTTGTAACTAATGCCTTTCCTTGAATGTGTTCGTCCAACGAAG
Seq C2 exon
GGAGTTTGCTTGGAGAGATCCAGAACTGCCTGAAGTCATTCACATGCTCCAACACCAGTTCCCGTCAGTCCAGGCGAACGCGGCTGCCTACCTTCAGCATTTGTGCTTCGGAGATAACAAAGTGAAAACAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012561:ENSGALT00000037713:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.687 A=NA C2=0.027
Domain overlap (PFAM):
C1:
PF0051418=Arm=PU(12.2=6.8)
A:
NA
C2:
PF0051418=Arm=PD(87.8=80.0),PF0051418=Arm=PU(14.6=13.3)
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:
GAGTTGGAAATCTGCAAAGATCATCC
R:
TCACTTTGTTATCTCCGAAGCACA
Band lengths:
342-1469
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]