GgaINT0071084 @ 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
chr4:45259779-45261105:-
Coord C1 exon
chr4:45260931-45261105
Coord A exon
chr4:45259933-45260930
Coord C2 exon
chr4:45259779-45259932
Length
998 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
TTCTTCAATGTTCATGGCAGACA
3' ss Score
5.83
Exon sequences
Seq C1 exon
ACGAAGAAAGGGAAGAATGATGATACAAGGAGGAAAGTCAGTGTGATGCTTCTAAGTGGACAGAAGCTGGAGCTGACCTGTGACACCAAAACAGTTTGCAAAGATGTCTTTGATATGGTTGTTGCCCATATTGGCTTAGTGGAGCATCACTTATTTGGACTGGCTAGTTTAAGAG
Seq A exon
GTAAGAATAAAAATTTTCTGGAGCAGATAGGTATAGAACAACGAGAGCTAACTACAGGATGTTGGGAATAATTGGAGGCTGCCTGGCATGTGCTTTGATGTCACATTGAGTTACACGCTCTTGTATTAGGCAAAATGCGTTCTTCAGGGAAGAAAATGTTTACTCAACAAAAGCCTGCATTTGTCTGAGTAGCAGCATCTCAGCTAGTTCTTTTTGGTTGCTGAGTGTTCTTCACTACTGCTTGTTGCCTTCACGTGTGTTGCTGTCTAGTGCCACACAGAAGATGTGAGCTGGGTTTTCTTGGTATGTTCTCGCAGCCTTTTCGGGGCAGCCCACAGGTATGCTGGGGCAAATGGTAGGGCCTCTTGTACAGAGTACATTGCCTTCAGACTAAATGAATTTATTTCTGAACTGTTCATTTTCTGCTGTTAGAACAGACCAGATGTTGGACTTCACTTTCCCCAAAGGGGAGAAGATCACTTTGGCAGCACTTACATATTGAGACCCACGTTTCCTGTTTTTGTGTCTAGCAGGATATCACAGAGCTGTAGCACTCAGAGTTCTGGCATGAGTCAGAAAACCTGAGCAGCCTGAGAGCCTTCTTCATCTGTGCTTGGCTCCCAGTGCCTTTGACAATTCAGCCATGAAAACGTTCTGTAGAAGTGTAAATTGGACATAAATAGTAAGGGAGGGAGGGAGTGGCAGATTAGGAATTAAGAAATTTGAGGGATACCGTGGTGCCTGATTCATAGCTATCATGGAATATGGTTTTTCTTTTTCTGCTCTCGTATTTTTTTGTTAACTAAAAAAGTATTTCTACTGCTATTGCTCAGTGTTCCCTTCAATAGCCATTGTGCTTACAAGCCATTGTTAGGACAGTAAGGTTTTCTTATGGCTGAACTGAATTCCAGAATTGGAAATCCAGTCCTGATCCTCCGGCTGGAAAAACGACTTCGTTCTGTTTTTACCCATGTCCTTTTCTTCAATGTTCATGGCAG
Seq C2 exon
ACAATGAATTTTTCTTCGTTGATCCTGACATAAAGCTGAGCAAAGTAGCTCCAGAAGGATGGAAAGAAGAGTCGAAGAAAAAGAACAAGCCCCCTGTCAACTTCACGCTGTTTTTTCGCATCAAGTTTTTTGTGGATGATGTCAGTCTTATACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011078:ENSGALT00000018050:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.034 A=NA C2=0.038
Domain overlap (PFAM):
C1:
PF093795=FERM_N=PU(49.4=74.6)
A:
NA
C2:
PF093795=FERM_N=PD(49.4=84.6),PF0037313=FERM_M=PU(5.1=11.5)
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:
ACGAAGAAAGGGAAGAATGATGA
R:
TGTATAAGACTGACATCATCCACA
Band lengths:
329-1327
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]