GgaINT0071096 @ galGal3
Intron Retention
Gene
ENSGALG00000011078 | PTPN13
Description
NA
Coordinates
chr4:47280773-47282300:-
Coord C1 exon
chr4:47281834-47282300
Coord A exon
chr4:47280908-47281833
Coord C2 exon
chr4:47280773-47280907
Length
926 bp
Sequences
Splice sites
5' ss Seq
AAGGCACAG
5' ss Score
0.29
3' ss Seq
TTTTTGTTTTTTTGTTTTAAATA
3' ss Score
3.28
Exon sequences
Seq C1 exon
CTTCGTGCAGCACCTCACACCTCACTAATGGAACCAGGACCTATGTAAGAAGACCATCATCAGTGCAGGACAATGAAGCAGAGTCCTCTTCGGAGGAGCCTAGCAGGTCCCGTGCTCATCAGAGAGCTGTTACAGGCAGTGTATCTGCCTTGTCAGGAGGCAGGCGGGATGGGAGTGTGAGCTCCCAGGACTCCAGGACTGAGAGTGCCAGCCTGTCCCAGAGCCAGACAGCCAGCTGCTTTGGCAGACGTGCTAGTGGCAGATCCCAGCAAGATCCGCAGAAGTACCCTGACTCCCAGTCCGGGGTTTTGAAAACTAATGAGAAGAGAAGGTCGTCATCGGACAGTACTCGAGCCAAAATGAAAAGGTCGGGAGTTGTGGAGTCCGTGGAGTATTCTGACCGAGGAGATTCTGACATGGATGAAGCAACTTACTCCAGCAGTCAGGAGCAGCAGGTTGCTCAAAAG
Seq A exon
GCACAGTTTATTTCATGTGAAAGTTTCCCATTGGTGTAATAGTGGCAGTGAAATATCTGTCTGTTGGTGTGAATGAGGTGAAAGGGGTATGGGGGAAGGGCAGCCTAACCCACAGTTTGTCCTCCTAATGGCAAATGCTGGTAACTTATTTCTACCAGTTTGGTGATTTTGTTCAAAATAAGTGAAGAAATTCACTCCTGGAATTTCAAAGCATTTTTCAACTTCACCATGTCATGTCATAGGCATGTCTTACTCAAAGCAGATTCTGCTTTGCAATGAATGTGTAATGCTCTTGTAGATTCCGTAAGAAACATCCATTCATTTAGTTTTGTCCAATGTGATCATAGTCTGATGACAGTCCTAAAGAGATAAGAAAAGTAGTACTGATGTAACTGAAATGAGAGCCTAGAGTAGCAAATGAACCTGTATCTTTTGACGTTGATCAAATCAATGGAAAAATGCTCTTATCTAATGAAACTTCATTCTTGTCTCGTGAAGCTCTGAAGTGAGCCATGCCCTGAGCAAACACATTCTTCACTTTGCTGAAGGTACACAGCAGAAAGTACTACAAATTTATCCCTAACCTATAATGATTGCTGTGTTCAATTTATGCAAATTAATACAACAGAACCTAGGCTGCTATAATGGTGAAGCTCTAGTTATGTTTTCTGTGTTCCATGACATTAAAGACTCAACTGCTGAAGGCCAAACGTGTTTCTGCACTAATGCTGTTTGGTTGCAGCTGTGGAAGAGTTAAAGCACTGCGTCTCATGTGCCATACAGATGGGTACTTTCCCATACGGAAACCTTTTGGCTGCAGCTGACTCAGAAACACATTCCTTAGGATCTTACCTGTACTATTCTGTTCTAACAAAAAATCTCTTTTTTCTTTTTTTCTTCTTTTTTTTTTTGTTTTTTTGTTTTAA
Seq C2 exon
ATAAAGGAATCTTCCTCAACAAATACAGCCGACAAAATGAATTCTAAAAAGGTTTCTGCAGAACTTCTTAAACCTGGAGATATCTTTGAGGTTGAACTAGCCAAAAAAGATAACGGCTTGGGAATAAGTGTCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011078:ENSGALT00000018046:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.444
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0059519=PDZ=PU(18.1=33.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg19)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGCAGATCCCAGCAAGATC
R:
GTGACACTTATTCCCAAGCCGT
Band lengths:
346-1272
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]