GgaINT0053598 @ galGal4
Intron Retention
Gene
ENSGALG00000009315 | PAPLN
Description
papilin, proteoglycan-like sulfated glycoprotein [Source:HGNC Symbol;Acc:HGNC:19262]
Coordinates
chr5:25602828-25604467:-
Coord C1 exon
chr5:25604291-25604467
Coord A exon
chr5:25602985-25604290
Coord C2 exon
chr5:25602828-25602984
Length
1306 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGC
5' ss Score
8.69
3' ss Seq
GCCTTGTCTCTGTGCTCAAGTGT
3' ss Score
4.07
Exon sequences
Seq C1 exon
TGCTCAGCCAGCTGTGGGGAAGGCGTCCAGACCCGGACTGTCACCTGCAGAACGCAGCATGGCTCTCAGGCTCAGGACTTTGCTTGCTTAATGGAGCCAAAGCCACCAGCCACGCAGCCCTGCCTTAAGGAGAACTGCATCCAAGAAGTCGGTTGGCACGTTGGAGACTGGGGCCTG
Seq A exon
GTAAGCATCATGCTTTCATGCATCGGAAATAATTGATTATATTGCTGTGTTCCTTGCAAACAAGCTTTAATCAGTGCAGCCTGCAATTGGCTGAATTGGAAAGCATGTACTGCTTCATTACCAGTCCCTTGGCTCACAGTTGCATTGTAACTGGCACTAGTAATGCTTCAGTTAATCTGTTGCCTGCTTTGTTTGCAGCTGCTATAAAAATAAATCCTTCTTGGAGGGGGAGACTATAGTTTCAGTGACAGCGGCAAAATGCAGCCAATAAACTGAAACGATCCACTCCTGCTGTTTATTCTCATTTATTTGCTCCATTACTGTGAGCAGCAAAGCAGCTCATGGGCTGAATATGGTTTAGAGCTTCAGGACTGGTCATCATGTTTGGTGAAATGATTTAAACTATGTTTTTGTAATTGTTCAGATAAACTGTTTTTCAGCTGGATTAATCTTTTCTACCTTGTGGAGGGAGACAGGCTGTTTTCAGCCTGGGAAACAAACCCGGGGGAGAAGATGGGGGAGACCCAGTCTACCATGTGACTTTCAAGCACACTTGTTTCTCTTCCATGCTAGTGAGACCAGCTTGTTCTGAGTTAAAACGTTACATCTGGTTCTTTGTTTGGTGTAGCTGAGTTTTAATAACAGCTAAGAAAGCTGCATAGCTTAATCTGATCTTTCCTGGCATTTCGTGTATCAGAGGGCTCCTACTTGTATCTGAATAAAAGAAAGGAACACTCTCCCAGTGTCTTAAAACTTTCCATGAACAGGTTGGTTCTCATCCTCTCCACTGCTCTCTCTACCTGGAGTTGCTGCTCGTTGCTTCCTATTCACTCATGGCTTCTAGTGAAAGGAACTCCAGTTGGCTGCTTACAAGAAAGCTACCCATTTGCTTTCCTGTTGTAAAATGCTGCCTGTTGTTTTTGAATTCAGAGTTCAAAACTGACCCTGTAACAACTGGTGGATGCCTGTAGTGCTGCAGTGCCCTCAGGCCAGGCTGGATCAGTTTACTCCTGCTGCTTATCCCAGCTCCTTGCCACACCACTGTCCTTGGCAGAGCAGCAAATCTAGATGTTAGAGAGTAAGCGTAGCTTGGAGCCTAATGCTTCAAGGCTGGGTGCAACAGTTGGCAAAATGATTAAGACTACCTCTGTTCAGATGAATCCAGCTGAACTGTTATTTGCCTGATCTTGGAGGAGGAAGCTGTGCTCAGCCTGCAGCTAATCACAGCTGTTCCACACTCCTGGTCTGTGGTGTTTCTGCACTCTGACTCTGGTTCCTGCTCACTTGCCTTGTCTCTGTGCTCAAG
Seq C2 exon
TGTTCAAAGAGCTGCAATTCAGGCATCCGGACACGCCAAGTTATCTGCGCTGATGGTGACTCCAAATTCTACAGTGCTGATATATGCAAAGCCATCCAACCACAGAAGCCAGCCACACTGGGTAGCTGCAACGTGCAGCCTTGCTACCTGCCACAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009315:ENSGALT00000015156:12
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=0.000
Domain overlap (PFAM):
C1:
PF0009014=TSP_1=PD(83.3=76.3),PF0009014=TSP_1=PU(10.9=10.2)
A:
NA
C2:
PF0009014=TSP_1=PD(85.5=88.7)
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:
CTCAGCCAGCTGTGGGGAAG
R:
CACGTTGCAGCTACCCAGTG
Band lengths:
310-1616
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]