GgaINT0053612 @ galGal4
Intron Retention
Gene
ENSGALG00000009315 | PAPLN
Description
papilin, proteoglycan-like sulfated glycoprotein [Source:HGNC Symbol;Acc:HGNC:19262]
Coordinates
chr5:25592325-25592956:-
Coord C1 exon
chr5:25592819-25592956
Coord A exon
chr5:25592453-25592818
Coord C2 exon
chr5:25592325-25592452
Length
366 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TTTCTGGTTTTGTCCATCAGACA
3' ss Score
6.88
Exon sequences
Seq C1 exon
GTTGAGAATGGACAAGAGCGAGCCCTCGGTAGTAGAGGCCAAAGTTGGGGAGAGAGTCAGACTGCCCTGCACAGTGGAAGCATCTCCAGCTCTCACCATTGAGTGGCAGAAAGATGGGCAGCCCCTCTCCCCTCCCAG
Seq A exon
GTGAGCTCCCATCTGGCTTTACTATTCCTGCGGCAGGCTGTGGGGAGGAGAGCCCCATTCTGAGGGAGCGCTGTTGCTGGCCAGTGCAGATAAGGCCTGTTCTGCTTTGTGCTGGGCAGTTTCATTTGTTAGGGCCAGACAGTGGTGTCCTACTGCCCTAGCTTCAGTCACAGGTCAGAGCCTGGACTTTAAGCTCTCATGTGAACAGCTGTGATACAGAGTCTACAGACAATAGGCCGTGTTGTGGATTGAACTGAGCTGCCGCTATACCTTTGCTTAGTGTTACTGCAAAGTTGTGCATAAGGCTCAGATTCATTTCTGGTGGCTTAAATTCAAGCTGAGGGGATTTCTGGTTTTGTCCATCAG
Seq C2 exon
ACACAGACAGCAGTCAGATGGGGCCCTGGTGATCAGCCGGGTTAGCTCTGAGGACGCCGGCTTCTTTACCTGCATCGCCTCAAATGGACGTGACCAGGACCAGCGCCAGGTCCTGCTCCGACCTTTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009315:ENSGALT00000015156:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.383 A=NA C2=0.273
Domain overlap (PFAM):
C1:
PF0767911=I-set=PU(50.6=89.4)
A:
NA
C2:
PF0767911=I-set=PD(48.2=90.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGAATGGACAAGAGCGAGCC
R:
CTAAAGGTCGGAGCAGGAC
Band lengths:
263-629
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]