GgaINT0071104 @ galGal3
Intron Retention
Gene
ENSGALG00000011078 | PTPN13
Description
NA
Coordinates
chr4:47273030-47274634:-
Coord C1 exon
chr4:47274466-47274634
Coord A exon
chr4:47273189-47274465
Coord C2 exon
chr4:47273030-47273188
Length
1277 bp
Sequences
Splice sites
5' ss Seq
CCGGTAATT
5' ss Score
6.28
3' ss Seq
GTGCTACTTTCTTCCCCTAGGAA
3' ss Score
12.02
Exon sequences
Seq C1 exon
CACTCTGCTGTTGGATTTGACATCGATCCCACCCTGTAGAACCATTCCTGAAGTTACCACATCTGCTTTAATAAACAGCTGTTATGCTACTTCTGAGCTGCCTCCACGCCTGGAAGGAGTGGCCTCACTACTCAGCCAGCTGGAAAAAAGTGCTGAAGAATATGAACCG
Seq A exon
GTAATTTCCTGTTTCTGTCTTTCAGTAGTTTAAGTGTAACCTCTGCTGTGGCAGCTGGATGTTTTTGTGGCCATAGTTTGGAGTGACTGAATAGAGAATAGGCATATTAATTTACAAATGTGGCGATTGTAGGTTATACTTGCACTGAACTGGGGATGTCTCATAAATGGCACTTACATTCTGAACTGTGCTCATACAGGTGTCTGCAGTTGTTTTCTCTCTGAGGTTTTCAAGGATTGATAATATTTCCCTCTGTGAGTATGAATGCATCCCTGTGTGTATAGGCAGATATGCATACATATATTTTGTGTCTCATTTTAGTCTAGAAGCTTGATGTTAAACATTTCCCTAGCTCTAGACAAGTTCTCAGACTGAACTTATATGCCAGTTACCTTGTTGTGTGGTTGGTTAGAGATCGTGGGATAAATCAGGCCAGAGGGGGCCTCAGGAAAGCCTGTTCTTTGCTGCTTTAATCAACATTTTGTGCTCTGCTGCAAAATGTAGCGTCGTTTTGAGACTCTTCTGAGATAGCTTCTTGCCACCCTGGAAACATTTTGCAGAGTGTGAGAAGGAGTTTGTGCTTCCATAGCCTCACATAATTGACTCACAAATAAAAAAGAATGTGACAGTTGAGCCTTGGTATGTTTCGGTTGTGGAAGCCTCCCAGGTTACACAGCTGTTCATGCCCATACTCCCTTTGGAGATCTAACAAACTGTCTCCTTTTTAGTCTCTTCTTCAGAAGTTATTCACAAACCTTCATGGCGTTGTGTGAGTGTCTGTTCATATGAAACAGATATGTATCTTTCAAATGGCAGTTCATGCAAATAAAAACAGAGAAGGTACATGCATGCGTGCAGTTCCCAGGAAAGCCATAGTTTTATCTTGTTGTAGGAAAAACTATTCACCTACTTCACTTGACTAGTTCCTGCTGTGCTGTCTTGCTCAAAGAGCCTTTTTATGTATGATAGCTAGTTCAGAATAAAGCAAGGTGCCAGTTTTGACGTGAGCCTTCACAACTCTGTTTAGATCATTAGGCCTTTGGTCCAAGGTCAGCTTCGTGCAAAAGAGCGTCGTGTCCAAATGAGAGACAAGTGCTGGATACAGCTGAGCTGGGCCTGCTCTTACAGATGTCTCAGTGCTATCCAGGCTTGTGTTCCAGTTACACCAAATGGTGCATTAGTTATCTATTTCTATTGGTGTTAAATTCAATTTGCCCATGGTCTAAAGCTGCTTCTGTTTTTTTTTTGTGTTGTTAAGTGCTACTTTCTTCCCCTAG
Seq C2 exon
GAAGTAGAACTCCAGGTCACCATGACCAAGTCTGAAAAGGGCAGCCTGGGCTTTACGGTGACCAAAGGGAACGATAACGTGGGCTGCTACATTCATGACATTGTTCAGGATCCTGCCAAAAGTGATGGGAGACTGCGACCTGGGGATCGACTCATAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011078:ENSGALT00000018046:32
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.088 A=NA C2=0.245
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0059519=PDZ=PU(60.8=90.6)
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:
CACTCTGCTGTTGGATTTGACA
R:
TTATGAGTCGATCCCCAGGTCG
Band lengths:
326-1603
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]