GgaINT0071080 @ 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
chr4:45270227-45272213:-
Coord C1 exon
chr4:45272118-45272213
Coord A exon
chr4:45270336-45272117
Coord C2 exon
chr4:45270227-45270335
Length
1782 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
CTATGCTAACTTGTCTTTTGGTT
3' ss Score
0.33
Exon sequences
Seq C1 exon
AGCCTCTGAGAAGGTACAAATCATACCACAGCGATGTTTACAGTACTTCGAGTGAAAGTCCATCCATTATTTCTTCAGAAGCAGATTTCAGGCAAG
Seq A exon
GTAAGATTTCTGCTTAAAAAATAACAGAATAAAAGAAAGTGAAGAAAATTGTTTGAAGAAAAATAAAAGAAAAAAAATGAGGGAAGTCTATATCTGTAGTAGGAGGCTTTATAATTACCACTAGTCTGAAGTTGTAAGATGATCTCATGTAATTACATAATTATGTACAATTCAGCACAATTGGCAGTCTGTGCAGAAATGAGTTTGACATTTCACACTCTGAAAGGGAACTTGTCAGGAAAAGGTGGAAATGGTTAACTTCCCTGGAGGACTTGGTCTAAATGGCATGCAGCCTTCCCAGGCACAAAAGCAATCAAGCTGTTGCTGTTGTACAATTGTAGTAAATTGCAAAAGCTTTATATGGAACATGTATGCTTTAATTATTTGGATTTCAGAAGGCTTCTCTGTGAGGATCAAATAGTTGGTAATTTATACGCCAAAAATTTTGATGTAATGCAAAAATGTCTACTATATGTATGTTGTACAAAATCAGTGGCTTGGTAAAGCAGGAGATGGTGTGAAGTGCTTTTCATTGACAAATGGCAGGAAGGTTTCCTTCCCACCATGGAAGCACAGCATGGAAAAGAAATACTTGAAGTGTTCTTTGGAGAAGTGCTAAAATGGTGAAAAGATGTGAGGAGAAGCATAGAGGATGAAACCAATAACCAGCTTGGCAAAGTCATTGTAAGTTGTGGAGATGAACCATTTTATCAAAATGTAAGAAGAAAACAATAGTCAGGAAATGAGTACAGCTGCACTGTGTGCATCCTGTATGCACTGCTCAACCCAGCCTCTCTGTACACACCACTCTCAGCTTTCCTCCTAAATGCTGAGCCAGAGCCTGGGAAGTGGAAGCAAGCAGCAAGTAACAATCTTGGTCTCGAAGCACAGCTCCTGTAACTCACTTCCCTTCTATGTCTTGCCATTCAGACCAGGCTGCTTGAGAATGTCTGCCCAGAGCCAAATGTTTATGAGTCTAAACAGGTGTGAGAGAGATACTTTTGGCTACCTGCACTGCTGGGCTCAGCAAAACAGCTGTAATGTAAAGAACAATTTCAAAGTCTGCATGACCAAGAACTCTCCTGCTGCCTTTGTTCATTGTGGGTACAGAGATGAAAGCAAAATGCTCTGCAAAATCAGACCCTAAGTGCTCACATCTCAGTGCTGCTGCAGAGGACTTATCAGCAAAAGAGGTGACTTGTGAACAGGAAAGCAACTAAGTCTGTTCCAAAAAGAGAAAAGAATGACCACTGTTTCATAAATCACAGAAAAGTGTCAGATTTCAGAGAGAGAAATTAAACACAGGAGCTCAGCAATATGCTGGTTTCCTAATTTCCTGCTTGTGAACTGCAGCACTGTGCTTTACCTAGCTGCTCTGATTCTGCTCCAGAGCAGTTTTTGATGGTGTCTCTGCCACTTTACATTTCGTGACTGAAAAAGAAACATTTCATGCTGGAAAGGTGTCTGTGCATTTGCATGCAGTTTTGTGGTTTTGATTGGATGAGGCTTACTTGTGTGGTTTTTTTTTTTACTTAATTAGGCTTGCCTTAGTATTCTTCCTCAAAGAGCTTGTGGTATTGTTACTTTCATTGGAGGAAGCAGTAAGATCTCTGAGAATTGAAATGACTGCATAAGGTTGCGTGCCTAATATCAGGAACATAGAAACCTGATTCCTTCTAAGTTGTCTTTGATGAAAATTAGTTAATTTCTGCTAAATCCTTAATTTTAGATGGGATTGCTCCTTATGCTTTGTTGCCCAGTCCTATGCTAACTTGTCTTTTG
Seq C2 exon
GTTTGCCAGTGAGAAGAAATGAAGGATTCAAGAGAGATGATGCCGGTGGTGCTTTACCAGGTGCTGATGATATCTCCACATCAAGTCAAGCTCATTCTCAGAGGGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011078:ENSGALT00000018050:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.479 A=NA C2=0.973
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:
AGCCTCTGAGAAGGTACAAATCA
R:
TGCCCTCTGAGAATGAGCTTG
Band lengths:
203-1985
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]