GgaINT0071083 @ galGal3
Intron Retention
Gene
ENSGALG00000011078 | PTPN13
Description
NA
Coordinates
chr4:47294353-47294711:-
Coord C1 exon
chr4:47294637-47294711
Coord A exon
chr4:47294528-47294636
Coord C2 exon
chr4:47294353-47294527
Length
109 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGA
5' ss Score
8.85
3' ss Seq
TTTTGTTTCATCAAATGCAGACG
3' ss Score
7.15
Exon sequences
Seq C1 exon
AATTTCTTTGGCCCTGAGTTTGTGAAAATGACGATTGAACCATTCGTCTCCTTGGATCTGCCAAAGTCTATCTTG
Seq A exon
GTAAGAGAGGGACTACTGAACAATTGGTGGCAGGGAAAATATATTTAACCAACGAATGCACCTTAACCATGAGTGTGAACACTGGGATATTTTGTTTCATCAAATGCAG
Seq C2 exon
ACGAAGAAAGGGAAGAATGATGATACAAGGAGGAAAGTCAGTGTGATGCTTCTAAGTGGACAGAAGCTGGAGCTGACCTGTGACACCAAAACAGTTTGCAAAGATGTCTTTGATATGGTTGTTGCCCATATTGGCTTAGTGGAGCATCACTTATTTGGACTGGCTAGTTTAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011078:ENSGALT00000018046:11
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=0.034
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF093795=FERM_N=PU(49.4=74.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTTCTTTGGCCCTGAGTTTGTG
R:
ACTAGCCAGTCCAAATAAGTGATGC
Band lengths:
242-351
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]