GgaINT0053589 @ galGal3
Intron Retention
Gene
ENSGALG00000009315 | PAPLN
Description
NA
Coordinates
chr5:28500598-28501060:-
Coord C1 exon
chr5:28501000-28501060
Coord A exon
chr5:28500701-28500999
Coord C2 exon
chr5:28500598-28500700
Length
299 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGAG
5' ss Score
7.1
3' ss Seq
ATGTTTTCTCCTCCAAACAGAGC
3' ss Score
10.48
Exon sequences
Seq C1 exon
GACAGAAAGTGCTTCCAGTTGCATTGGACCAACTCGAAGCTATCGCTCATGCAATATTCAG
Seq A exon
GTAGAGTACAGTGTTTGTACTCTGTTTTTTGGTTTTTTTTTTTATTTGCTTTCCTGTTGCTCCTTTTCCCAAGACAAATCATTCATGTTCAGAAGTAATATGCTATTGTTAGATTCTCTTTCTCTGGCATTACTGATGAATGCTGTTCATCAATGGTACCTCTTCAAAAGAATATTGATCCCAGACAAGAATTTATCTGAAGATTTTATGTGTGAGTCAGAAGGGGCAGTTTTTAGCTGCCCATTTAATTCTCCTCCTTTTCCTCATGGCCTGGTGAAAATGTTTTCTCCTCCAAACAG
Seq C2 exon
AGCTGCCCAGAAGGCTCCAGAGATTTCCGAGCAGAGCAGTGTGCAGAGTTTGATGGGACAGAATTTCAAGGAAAGAAATACAAGTGGCTTCCTTATTATGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009315:ENSGALT00000015156:3
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=FE(40.0=100)
A:
NA
C2:
PF0009014=TSP_1=PD(2.0=2.9)
Main Inclusion Isoform:
NA
Other Inclusion 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:
GACAGAAAGTGCTTCCAGTTGC
R:
CTCCATAATAAGGAAGCCACTTGT
Band lengths:
164-463
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]