GgaINT0053613 @ galGal4
Intron Retention
Gene
ENSGALG00000009315 | PAPLN
Description
papilin, proteoglycan-like sulfated glycoprotein [Source:HGNC Symbol;Acc:HGNC:19262]
Coordinates
chr5:25591702-25592452:-
Coord C1 exon
chr5:25592325-25592452
Coord A exon
chr5:25591811-25592324
Coord C2 exon
chr5:25591702-25591810
Length
514 bp
Sequences
Splice sites
5' ss Seq
TAGGTACCA
5' ss Score
3.96
3' ss Seq
CTGTTTACCTTCTGGTTTAGGAG
3' ss Score
9.6
Exon sequences
Seq C1 exon
ACACAGACAGCAGTCAGATGGGGCCCTGGTGATCAGCCGGGTTAGCTCTGAGGACGCCGGCTTCTTTACCTGCATCGCCTCAAATGGACGTGACCAGGACCAGCGCCAGGTCCTGCTCCGACCTTTAG
Seq A exon
GTACCACGAGGGTGGCAGTGTTGCATGTTTGCGTGCGCAACTGTGGAACAAAAAGGGCTGGGCAGAGTGGGTTTCTCCTCCGGCCATGCCTCTTAGCTTCACACCTAATGTTTAACAGGCAGCTTGTCGGTAAGGGAAGAGTGAGTTGTTTTTCCTGATGGTAATGTACGTAGTAGGTCATGGTGCTCTAGAGAGCTGAGGTGGGACTGCTTGCATGAGAGTGTCTCTTGGGCTTCATTTCTGGCATGGAACAGGTATGCTAGTAGCAGGAGGCAATAAAGAGGCAGTTCTTCTTTGTGTATGATGTACTTTTGTCTAACTGCAGGAAAAAAGCAACTCTTTGAAACCTCCATTTCTTGCCCTGGCTTGGGCTAAAGCCCTTAGGAAATACGACATTCCCTGTAGTAATAGCTACAGTAGTTTCAACATGATGGTTCAAGGCCTTAGAAGCTTCTGCTACCAGGGGCAGCATAGCATTGTATTCTTGCTAGTAACTGTTTACCTTCTGGTTTAG
Seq C2 exon
GAGGGCTGAGGATTACTGGTCTTCTGCCAAGCATCAAGGTATCTGAAGGAGAAACTGCTCAACTTCATTGCACAGTGACTGGCAACAATGTGAATATAAGGTGGTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009315:ENSGALT00000015156:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.273 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(48.2=90.9)
A:
NA
C2:
PF0767911=I-set=PU(39.1=91.9)
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:
GACAGCAGTCAGATGGGGC
R:
TGACCACCTTATATTCACATTGTTGC
Band lengths:
230-744
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]