GgaINT0071095 @ galGal3
Intron Retention
Gene
ENSGALG00000011078 | PTPN13
Description
NA
Coordinates
chr4:47281834-47282722:-
Coord C1 exon
chr4:47282591-47282722
Coord A exon
chr4:47282301-47282590
Coord C2 exon
chr4:47281834-47282300
Length
290 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
TCTTCTCTTCTGGCTTTCAGCTT
3' ss Score
9.16
Exon sequences
Seq C1 exon
GACACCGACTGATATCTGTGAACAGCACAAGTTTGGAGGGCGTCAGCCACCACACAGCATTAGAGATTATAGAGGATGCACCTGAGGATGTAACGCTCGTTATCTCTCAGCCCAAGGAAAAGCCATCCAAAG
Seq A exon
GTATGGAGAGGAATATTCCTTAGTATTAAACCACTGATCTGAGCAGCTGACCTGGCCGTACATCACTTCTGTGCACCCCAGTTAATATGTGCTTACAGTTGTGTTAGAGACTGACAGCGGAAGCGTTAACCTTTACAGTAGGATCATTTGGAGTAATTTTCAGTGATGGCACACTGGTTGCACCTTAAATAGAAAGCGTTATGCATGGTATAGAATGGTAAAACCTCACATGGCCATAAACTAAGAGATGTGACCAGTCCCTGCTGACTGTCTTCTCTTCTGGCTTTCAG
Seq C2 exon
CTTCGTGCAGCACCTCACACCTCACTAATGGAACCAGGACCTATGTAAGAAGACCATCATCAGTGCAGGACAATGAAGCAGAGTCCTCTTCGGAGGAGCCTAGCAGGTCCCGTGCTCATCAGAGAGCTGTTACAGGCAGTGTATCTGCCTTGTCAGGAGGCAGGCGGGATGGGAGTGTGAGCTCCCAGGACTCCAGGACTGAGAGTGCCAGCCTGTCCCAGAGCCAGACAGCCAGCTGCTTTGGCAGACGTGCTAGTGGCAGATCCCAGCAAGATCCGCAGAAGTACCCTGACTCCCAGTCCGGGGTTTTGAAAACTAATGAGAAGAGAAGGTCGTCATCGGACAGTACTCGAGCCAAAATGAAAAGGTCGGGAGTTGTGGAGTCCGTGGAGTATTCTGACCGAGGAGATTCTGACATGGATGAAGCAACTTACTCCAGCAGTCAGGAGCAGCAGGTTGCTCAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011078:ENSGALT00000018046:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.911 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0059519=PDZ=PD(41.7=77.8)
A:
NA
C2:
NO
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:
GTCAGCCACCACACAGCATTA
R:
CTCTCAGTCCTGGAGTCCTGG
Band lengths:
296-586
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]