GgaINT0071097 @ galGal3
Intron Retention
Gene
ENSGALG00000011078 | PTPN13
Description
NA
Coordinates
chr4:47278853-47280907:-
Coord C1 exon
chr4:47280773-47280907
Coord A exon
chr4:47278947-47280772
Coord C2 exon
chr4:47278853-47278946
Length
1826 bp
Sequences
Splice sites
5' ss Seq
ACGGTACTG
5' ss Score
5.88
3' ss Seq
CATTTTTGCTTTACTTTTAGGGT
3' ss Score
9.97
Exon sequences
Seq C1 exon
ATAAAGGAATCTTCCTCAACAAATACAGCCGACAAAATGAATTCTAAAAAGGTTTCTGCAGAACTTCTTAAACCTGGAGATATCTTTGAGGTTGAACTAGCCAAAAAAGATAACGGCTTGGGAATAAGTGTCACG
Seq A exon
GTACTGTTTGACAAGGTTTTCAGATGTTTTCTCTTTTTCTCTACTCCCATAACCCATTAAATTACTAAATTCCAAGGAAGCAAAATATTTTCTGGAGTCACTGCAGAGCATGTAGTTTTACTGACTTACAATTAATCTTATCAGAGCTGAAAAATAGTGTGGTAAATCCTTCATGTCATCTCCCCTTCAGGTAACCTTCATTTGATGTTTTACAACGAAACCCCAAAGTCGAAATAGAATCTTATCACAACAGCTGCTTTGCAAGTACAAACAGAAAGATGGGCTTTGTCCCTTGCTCCCCAGTAACATGGCGAGTTTGCAAGGGGGAGAAATTAGAGCTCTCCTGCTGGGCATCACATGCAGAAATGGGGTTGTGTTACCTCAGAGTATTTGCACTCCACGCACACATACTGTGTTGCATTCTCCCTCTGCTGGTTAAAAGGTAGAAAGCAAAAAACTACTGAGATGCAACTTAGACCTGTCTGGCATTGCCTCCTTGCAAGGTTACTGCCCTTAGGAGACAAAAATGTACTTTTAATGGATGAATTTCTCATCAGGTTATAAAATTTTGATGGTGATTCGCACTTATGGGCTGCCATACCTCACAGTGGCACTTCAGAGATGAAGGGAATGAATCAGAACTGATATGTACACGTCTTTCACTGCTCTGTTTTTGTTTTGTGTTCAGAAATGCATCTGAATATTTTAATATTCCAGGATTATCTCTGGTTGATAGATCAGCAGACTATGCAATTATTTGAGAATGGAAAAGTAGCATAAATTATAACAATAGAGAGCAGCTATTAACTGTAGATCAAATCTGTTGGGTTTTAGTGGCTGCTTATATCTAAACCAAGTCATTCTTTTCTTGAGTGTGGCAGTGTGGATAGGTATATGGGTGGAGTTGGAATTTGTAACCACTGAAGTCACATTGCTCTGTCAAGCTCTCAGTGTGAAGTGACTGGAGGCACAAAGGGTGAGCAGTACACGGTTACTGAACAGCAGCAAGCCTGCAAAGCCTAGGGCTTTGCAGAAACCATCACAAAATGCCAACAATGCAATGATTGGCCTTGGAGGATTACCAAGTAGTGCCTTCATTGTGCTTTCCTTTTTCAGTCTCCACACTGAGCCTTGCACTCCCATCCTGCATAGTGGTAAAAAGAAGAGGGACACAACTAGTTCTGTGCTTTAATCTTTCAGATGCAGCATCACACACTTTCGGAGTGAACATTAACATTCTGTTGGTCTCCTCCCTCCCTCCAGTTTGTGGAGCAGCTCTGACAGTGCAGTGTTGGCTGTCTGAGAGCCTGGAATGCAAAGGCCCTCAGAAAACAGTACCATTTGAGCTCGAACAGTTTTTTCAGTGTAGACCTTCAAAGTTCTATGACCTGAGAGAAAAGAAGCACTCCTCAGTTTGTGTTACATCAGAGGGTGAATTGGAGTAGGACACTGCATGGGATTCATCTCTTTGGCTGTTGCTGCTGGATGTGCTCACACAGTTTTTGGAGCTTTGTGTGCATGCAAGCATGTTAACTCCAGCACAGCAGACATGCTTTGCTGCAGGATACCTCTTTGATTGGAGTGCATTTGCATTGTGATGCATTGTGTTTGTACAGTCTTCCACCCTAGCCTGACTCATAGCAAATCGCATGACTGTGAACTATGCTTTGTAAAATGTTTTTGTTTGACAATTTGGCCTTTCCTTTTATGTGCCAGTAGCCAAAGTGCTTCCTTGAGTGCAGCTATCCTTGTAGTGTGTTGAGTTTAATTACAAAGTGTTCTAGCTGTAAAAAGACTGACAAATCCCATTTTTGCTTTACTTTTAG
Seq C2 exon
GGTGGTGTAAACACAAGTATAAAGCACGGTGGTATTTATGTGAAAGCAGTTATTCCAAAAGGAGCAGCTGAAGAAGATGGCAAAATAGAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011078:ENSGALT00000018046:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.444 A=NA C2=0.281
Domain overlap (PFAM):
C1:
PF0059519=PDZ=PU(18.1=33.3)
A:
NA
C2:
PF0059519=PDZ=FE(37.3=100)
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:
GGAATCTTCCTCAACAAATACAGCC
R:
TTTTCTATTTTGCCATCTTCTTCAGC
Band lengths:
222-2048
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]