GgaINT0071090 @ 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
chr4:45253331-45254024:-
Coord C1 exon
chr4:45253601-45254024
Coord A exon
chr4:45253429-45253600
Coord C2 exon
chr4:45253331-45253428
Length
172 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
CTCTCCTTCTCCCCTTTAAGTTC
3' ss Score
9.95
Exon sequences
Seq C1 exon
AGCGAGCTTCCTTTAGGAGCCTGAACATCCATGCGGAGTCAGTGAAAGGCTTTGGCATGGGGCGGGCCATCAGCACGGGCAGCCTGGCCAGCAGCACACTGAACCGCCTTGCAGTGCGCCCTCTATCTGTGCAGGCGGAGATCCTGAAGCGACTATCCTGCTCTGAGCTCTCGCTCTTCCAACCACCCCCTGGCTCTTCAAAGGACAAGAATGTAAAGACTTCGTGGGAGGAAAGACCCAGGGTGATTAGCAAATCGTTCCATGATCTGAGCCAGAGCCATATCTCAGTTTACCCTCCGAGGAAGAATGTTATCTCAGCTTTGGACTCTTCCTCCCAGAAAATAGAGGACTTAATGGGAAGGGTCTTTCAGCGAATGCCAAAATTTGATACTGGATCAGCAGCAGGAGCATTAAAACTGAACAA
Seq A exon
GTAAGAGTCTCTCTGAGCACCCTGAAATTCCTTTGTGTACATTTGATGTACATTTTGCATCGGTTTTAATTTATTATTCATACCATTATTTTATTACACTGATCCTTCCCTTCCCTCTCCCAATTTCCTTTTCCCTCTGTCTGATTTCCCTTCTCTCCTTCTCCCCTTTAAG
Seq C2 exon
TTCAAAATCTCATGCAGGTTTAAGTAGAAGTCCTGAAAGAAAGAAAAATGAATCGGACTCATCATCCATGGAAGATACCGGGCAAGCCTATGTTGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011078:ENSGALT00000018050:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.239 A=NA C2=0.971
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
TCCATGATCTGAGCCAGAGCC
R:
TGCCCGGTATCTTCCATGGAT
Band lengths:
250-422
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]