GgaINT0071077 @ galGal3
Intron Retention
Gene
ENSGALG00000011078 | PTPN13
Description
NA
Coordinates
chr4:47327855-47329644:-
Coord C1 exon
chr4:47329459-47329644
Coord A exon
chr4:47327949-47329458
Coord C2 exon
chr4:47327855-47327948
Length
1510 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGT
5' ss Score
9.65
3' ss Seq
TGCTGCTGCCTGTTTTGCAGATG
3' ss Score
9.63
Exon sequences
Seq C1 exon
CCTATCAAGCTTGGAGATCATCTCAACAGCATCCTCCTTGGTATGTGTGAAGACGTCATTTATGCCCGAGTATCTGTACGGACCGTTCTGGATGCCTGCAGTGCTCATGTCAGGAACAGTAACTGTGCCCCATCTTTTTCATATGTGAAGCAGTTAGTAAGACTGGTCTTGGGAAGCCTGTCTGGG
Seq A exon
GTAAGTCTTCATAAGCATTTGAGGATTAAGGGAGGTGGGCAGGAAGAGAGAAACGATGCTAAATCAGAGTCACTCTGCGGTCATTCTTCCTCTTGTTTTACCATGCTGCAATTCTGATAAGAGGGAATGCTGAAAGGAGAAAAATTCTGAAATCCCAGGAGGGAATTGTTTCTTTCTCCACTTAGCAGTTTGTGCAATCAACAGTTCCTTCTGGAATATAGATTCACAGCTGCTGTTTCTGAGAAAGATACTTTTCTGAAATGATTGTCCTCATTGGAAGAAAAGTAGAGAAATACGTAGTCTAGGGCAAGCATTAGACCTGTCACTATTTAAAATGCTGCTAAAGTGATCACTGTGAATTTTCTTTTTTAAATGTATGCTTGACTTTTGGAGGGGCACTGATTAATGGGGAGAAGGACTGAGTCATCGGTGTGCCAATTCTCTTGCATGTCTCCTCACCCCTGCGATACGATGACTGTAGGGGAATTTATTGTCAAATGATGACCAATGCGTTGAGCTGTTTTAAGAAGTGAAACGCGCTGCATGCAGCCGTCCTGCAAAGTTACTGTTCTTGACAGGGGCATCTCCCTTCATCTGAACCACCACAGCGTGGTTACAGAATAGCCACATAATTTCAGGCTCTGAAAACAACCAAAGGTTTTGTGTTGTCAGTATCACTAAGATTGTTCTTTTCTCAGTACTTACTTTTCTTTGTGCTCTGTTTGTAATTCCAACAAATGCCAAGCAGTATGTTTTTACTGGAATTATATGCCATTATGGTATTGGTTTTATTCTGTTTTATCCTCTTGGAACACTTCTATCTCAGAGGGGTTATGTAAATGTAAAAAACAAGTGTGTAGATGTACAGTACTGTGATTACAAAAAAGGTATTTGATCTCAGAGTACTCTCATTATAAAACATCCATTGTTATTTAATGATTACATAGATTCTTTGCACATTTAGTTTGGAAGTTTCTGCATGAGGTGATAGGTCTCTGTGTTTGTGTAATAGTCAGCAGAAGCTGTTGATGACTGGCCTCTAGAAGCAGCACTGAGCCTGAGCTCCACAAAGCACTGCCTGGACTGTGAAGTTATGTCTGTCAGGCTGGTGCTCTTCATCACAGTATCTGATTTCATGAGCCAGGTTGCTAAGTTGGTCTGTTCTGGGTTGGAATAAAAGGAAGACCTGCAAGACCTTAGGCACTGAAGCTATTAAAATAAAGAACCAAACTTTAAATCAGGCCACAAGCTATAGAAACGACCAGGGAGAAGAATGAGCCATTTGCCTTTAGATTCTTAATGCCCCTTTTTTGCTTAGCAAATGTTCTCCTTTTCTGCTCAGCTTGTTCTTGTCAGCAGGTGTGAAAAGGGCGTCTGAGGCCAATGTGAGGGGCTGATCTGGCTTGGCCAGCCAGTGATGGCCATATTGGTTATCATGCATATCCTGAGGTACAGTCATACTGAATCCAGCTGGCTTGTTCCTGACTTTGTGCTGCTGCCTGTTTTGCAG
Seq C2 exon
ATGGATCAGCTTTCTTGCAATGGAGATAAAAAATTGCAGCCAGACAGGAGCCAGGCAATTCGGGAGAGGCTGAGGGGAAAAGGACTGCCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011078:ENSGALT00000018046:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.562
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CCTATCAAGCTTGGAGATCATCTC
R:
CTGTGGGCAGTCCTTTTCCC
Band lengths:
280-1790
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]