GgaINT0071080 @ galGal3
Intron Retention
Gene
ENSGALG00000011078 | PTPN13
Description
NA
Coordinates
chr4:47303649-47305635:-
Coord C1 exon
chr4:47305540-47305635
Coord A exon
chr4:47303758-47305539
Coord C2 exon
chr4:47303649-47303757
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:ENSGALT00000018046:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.606 A=NA C2=0.973
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA

Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
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]