GgaINT0071114 @ galGal3
Intron Retention
Gene
ENSGALG00000011078 | PTPN13
Description
NA
Coordinates
chr4:47263415-47264930:-
Coord C1 exon
chr4:47264827-47264930
Coord A exon
chr4:47263564-47264826
Coord C2 exon
chr4:47263415-47263563
Length
1263 bp
Sequences
Splice sites
5' ss Seq
AAGGCAAGA
5' ss Score
2.81
3' ss Seq
GAGCCTCATTATTCTGCCAGATC
3' ss Score
5.1
Exon sequences
Seq C1 exon
ATCTCCTCCACAGCCTCCCTCGAGTCAAGCAGATGAAGATGAAATCACGTGGGGAAGTGATGAATTGCCAATTGAATCAATCAGCCAGGAACGTGTAAATAAAG
Seq A exon
GCAAGAGCTTCGGCAAACAGTTAATTGAAAACTGAGGATCACATTAAGTAGCCAATATGTCAGATGTGAATTTTAAAAAGTCTTGGATATGGTTTGAGGGTCTGATGACAGATATAGTGGGAAAACTCGATGGCTCACTGGAAAGAATCTTTACAGCTTGAAGTGATGTGTCTGAAAGTCCATTGGGGCACATATTGGTGAGGTTGGGGCTATGATGAGAGTGGAGTTGAAAGCAGCTTTCCTCCACCTGTCAGACAAAACCTTTCACAATAAGTGATGGTTTGCAGGATTTGGTTGTGATCAAATCAGTGTCTTGTGTGCTTGAAATTTTACCTGCTCAATGTTCACATTGTTCGCTATCTTCCCAATATATGGACTCTTATTTTTCCACTGTTGCTCAGTTTGGCAGGGTAGAGTACTGCTAAGTTGGACGCATTTGACAGATAGTAGTCTTTACTTTTTGAGAATTAGAAATGTCAAGTCCTGTAATCCTTATACAGAAGCCCTTTGTCTCTAGTGTGTGTATTCCTTGGTAGAAGAAAATAAAGATCAGTGTAAGCCTTGTGACTAAATCTACTAATTTAGGACACTTAAATGCAGTAACAGGAAGCCCTCAAGTTTGTTAATTTTGCCATGTTTCTGAGGAGCACCAAGGGCCTGATAGAAGCATGCTTTGACAGAAAAAATAAGATGTTTAACGTGTCTTTTAAATGGTAATTGTAAGATATTTTTTACTCTAAGTGCTACAAATGGGCACTCAGTTAAATGTTTATTTAACTGAGAGTTCTGAACTCATCTCTGTGCACATTCATGGATTTTGTGTTGATTTTGTTTTAAGAACTTACATTTAAAGTGCATATGGAGTTTGTTTCATTTGTTTGGTGTTCAGGAAAATCCTCTGTTCCCAGATTGATCAAAGTCAGTTTTGCTTCTTGCTGGTTATGTTGGTTAATTGGTTTTTGTCCCTCAAACTGAGAAGCTCTTTGTATGCTCTCTGGGTTGTATGGAGGGATTCTGAAGATAACAGGAAGCAAACTGTGTTGGAAGGACTGTTTCAATCACAGATTCTCTATTGGTCATAGCTTTCTGTGTAAGAGGATACATAAGAGGCAGCCTTTCATGGCAAGAAAACCATCTAGTACAGTAACAAGGACGTGCAGCGTTACACTACATTTTACATATTTCCTTCCTTTAGTTATTAATTTAGTTTAGTTTAGTTCATTATTTACACAGCCATACAAATGAGCCTCATTATTCTGCCAG
Seq C2 exon
ATCTCCCTCTGGTGACAAACGAAGAGATCTCCATGCTCCGTGCTGTGAGCGTGCTCCCTGGCGGCAAGTACTGCGGAACAAAGCTGAAGGCGGCCATCAGGGTACTGCGGGGACTGCTGGAACAGGGGGTTCCTTCCAAAGAGATCGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011078:ENSGALT00000018046:42
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.903 A=NA C2=0.050
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Skipping 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:
ATCTCCTCCACAGCCTCCCTC
R:
CGATCTCTTTGGAAGGAACCCC
Band lengths:
251-1514
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]