GgaINT0053609 @ galGal3
Intron Retention
Gene
ENSGALG00000009315 | PAPLN
Description
NA
Coordinates
chr5:28481922-28483078:-
Coord C1 exon
chr5:28482911-28483078
Coord A exon
chr5:28482050-28482910
Coord C2 exon
chr5:28481922-28482049
Length
861 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
GATTCCTGCTCCTGTTGTAGGCA
3' ss Score
8.17
Exon sequences
Seq C1 exon
AGGGGTCCCTGTAATCCCTTTCTCTTTCAGAGCCATTCTGGAGGAAGCCAAGCCCTCTCTTGTGACAGCAATCATGGGACAAAACATCCAACTGGTCTGCAAGGCAAGTCTGTCCCCCTTCTCCAGGGTGGAGTGGATGAAGGATGGCCGGCCAGTCTCCTCTGACAG
Seq A exon
GTGAGCTGAGCTCCCTTCATTACAGAGCAGTTCGTGGTCCTTGCTGAGCAGAGTGCCAAATATGCTTGCCCACTTTCTTTCTAATCTCATTGCTAACATTCTTTGGAGGGGATAAAAAGGATTAATAAATAAACAAGCCCATGTATTAACCTGGGAACACCCCTGAAAATGAGCTATCCCCCTGATCTATAAACAGCAGAAACAGGTATACTCTACAACTGTATTGAGGCACCAGATTGCATTTTGGGACAGAATGGGTGCTGCCCCAAAACCAGTAGGAACCGACATGTGGGCAGTTATGCAAAAGAATGTTGGCTGTGTAGGATTTTTCCTGGGACACTACTTAACTAGTCCAGGATGAAGCCTGTGGCCAAGTAAGTCAGGAGTTCCCCTGTCTGGAAGTTTCTGGCACTGCCATTTAAGATGCAATGCTTTTAAAATTATTTTTAAAGCCTATTTTTCATGGGAAGTCTGTTTCTTGCAACAGTTTGGATCCAGAGAGTCAGTTTTTGTTATGAAAATCATAGTTGTTAAGAAAAGCTCAGTTCTGCTTTTCTGTTTGCAAATGACTGCTGGGGCTTAGGCTCCTGCCTGAAAGGGCAGTTTGCCTTCTTATGGGAGAGGATTGAAAGCAGTTCCCTGTTTTCCCATTCCTCTCTGTTTCTGACCTCCTTTCTGTTGCAGTGATTTTCCCCTGCCTGTGACCCTGCTGTGGTCAACAGGGTTTTGTTTTTTTTCTCTAAGCTGGGGAGGGCACTGCATGATGGTGGTTTACGTAACATAAGCAGGAAGGGTTGCTCTGCCTTGGCCAGTTGCTGTCCTTGGCCAGGCAGAGGCAGTTGATTCCTGCTCCTGTTGTAG
Seq C2 exon
GCACACCTACCAGTCTGACAGCTCTTTAGTTATCAGCCACGTCAAGCTGGAGGATGCTGGGACTTACACATGCCTCATTTCTGATGGAAGGACAGAGAGTCGGCGGCAGATTCAGTTACAGATCGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009315:ENSGALT00000015156:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.123 A=NA C2=0.091
Domain overlap (PFAM):
C1:
PF0767911=I-set=PU(49.4=71.9)
A:
NA
C2:
PF0767911=I-set=PD(49.4=93.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGGGTCCCTGTAATCCCTTT
R:
ACGATCTGTAACTGAATCTGCCG
Band lengths:
294-1155
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]