GgaINT0071083 @ galGal4
Intron Retention
Gene
ENSGALG00000011078 | PTPN13
Description
protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase) [Source:HGNC Symbol;Acc:HGNC:9646]
Coordinates
chr4:45260931-45261289:-
Coord C1 exon
chr4:45261215-45261289
Coord A exon
chr4:45261106-45261214
Coord C2 exon
chr4:45260931-45261105
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:ENSGALT00000018050:12
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=0.034
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF093795=FERM_N=PU(49.4=74.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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]