GgaINT0053599 @ galGal3
Intron Retention
Gene
ENSGALG00000009315 | PAPLN
Description
NA
Coordinates
chr5:28488623-28489486:-
Coord C1 exon
chr5:28489330-28489486
Coord A exon
chr5:28488718-28489329
Coord C2 exon
chr5:28488623-28488717
Length
612 bp
Sequences
Splice sites
5' ss Seq
AACGTGAGT
5' ss Score
9.54
3' ss Seq
GTATATGTCTCTGTTTGCAGAGG
3' ss Score
8.95
Exon sequences
Seq C1 exon
TGTTCAAAGAGCTGCAATTCAGGCATCCGGACACGCCAAGTTATCTGCGCTGATGGTGACTCCAAATTCTACAGTGCTGATATATGCAAAGCCATCCAACCACAGAAGCCAGCCACACTGGGTAGCTGCAACGTGCAGCCTTGCTACCTGCCACAAC
Seq A exon
GTGAGTTGATTTGATAGACACACAACTTTTTCTAAGTTGCTTCTGCTTAGGAGTAGAAATTGCCAAGTCTTTATAAAAGCTTATGCTCTCAGCTACCTGCTTACCTGTCTCCATCCCGTGCTTTTGCACCTACAACCATAGCATCTTCAGAGTCCCAGTATCTGTGCTGTTTGAAGCACATGTTATGGATTTGGGAGCAATATTGGTGTGTGCCATTCTGAATTCAGTGTTTTGCCTTGACTCTGTCCCAGTATGTACTGCAGACTGACCCCACAACTCAGAGAGCTAAGGACTAACACCCTGGACAGGCTCAGTAGTTAGAAACTATAGCCAGCTCTCATCCCCTTGTGGACCAGCTGTAAACTGGACATTTTACTTGCTGTCTGTATTTAGTCTTCATGCCAGAGCTGAAATGGTGACTTCTGTCTGCCTACCTGTTGCAGGTAGCTGTCCTGACAATCCAATTGAATCCAATTGCTGATCAGCAGCTGTTCCAGGAGAAGAAACGCATTTTTGTCTACCTTAGTCTCCAGTTATTTTTCTGATGCGTTTGCAATTATTTGAATATAATTGGACTAGCTGCACTTATTTTGTATATGTCTCTGTTTGCAG
Seq C2 exon
AGGTCCCCAGTATGCAGGACACTATGGGATATGATACCAGTCGACGGTCCTTGCTGACGCGTTACAACCCAGACAGCCCTCCCACAGGTTCAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009315:ENSGALT00000015156:13
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=0.812
Domain overlap (PFAM):
C1:
PF0009014=TSP_1=PD(85.5=88.7)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTCAAAGAGCTGCAATTCAGGC
R:
GGAGGGCTGTCTGGGTTGTAA
Band lengths:
238-850
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]