GgaINT0071100 @ galGal3
Intron Retention
Gene
ENSGALG00000011078 | PTPN13
Description
NA
Coordinates
chr4:47276557-47277755:-
Coord C1 exon
chr4:47277593-47277755
Coord A exon
chr4:47276772-47277592
Coord C2 exon
chr4:47276557-47276771
Length
821 bp
Sequences
Splice sites
5' ss Seq
CAGGTCTGG
5' ss Score
5.06
3' ss Seq
TGCTACCGCTTCTCTTACAGAGA
3' ss Score
9.12
Exon sequences
Seq C1 exon
GTGGTGCATCTGCTTTTGGAAAAAGGACAGCTTTCGGTGACAAAGGCTCATGCTCCAGTAACACCACAGTGCACGCCTCCGAATCTGGCGGGGCCATGTGAGCCTCAGGAGAAACCAGCAATAAGAGCTACAAACACCAAAGACTACAGCTTTGTCACTGCAG
Seq A exon
GTCTGGCCATGTAGGAAAACACTGAAGGCATCCTTGAGTTTTATATCATTGTTTTTCTGTATCTCCTGTGAAATAGGAAGACAGGAGCCAGAGCTGATTAGGAATCCATAGTAAGCCCCTGCACATCATGCAATTTTTGTGTTTCTGTGCCATTGCAATTGGTTTTGAAGGTTTCCTTTCACATCTTGTTAACACAGTTCAGTGACTATGAACTGTTTGCTCTCACTGTTCCTTTTTTGTACCCAATTTTGCCAGCAGGCCAGGGCTGTAGGATTGTTGAGGTAGAAGGGCGCTGTTAATTCTGGTGCTGCTAAGACAAATGTATTAAGCGTGGATTAAATCCTCATAGAAAAGTGAGAGTTCCTGTTATATATAACTGCTGCTCCTGTCTAGATGGAAGCAGACATCCAGAGTTAGGTCTGGAGAAGGGCTAGCTGTCTGCCTGACCGGAGGCTGATATCTCAGCTCCTCCTGCTGCAGAGCTGTGCAAAGGAAGGGGAATCTGCATGTGAGGAGACTACTGCTGGTACCTTTTGGTCTGCCTTCCTGGGCAGGGTGTATCCTGCCTGCCAGGAGCTACAGTTGCTGCTCTTGCAAGTGTCTGCTCAGTGGCCAAAACAGGCACATTAATCAGCTATGACAGTCTCTTTAACGGGCTTCTGGAGAACTAAACTTTGGGGACACCTCCATGTGCTGCGTGGTGTGGTGTTAGGAAGGCAAGCTATCAGCCGGAGAACATCGTGGCTGAAGGCATAGTGCACACCACTCATTTTAATGGCCAGTGTGCTGTAGGAAATAATGTGCTACCGCTTCTCTTACAG
Seq C2 exon
AGAACACATTTGAGGTAAAGCTGCTGAAGAACAGCTCAGGTCTCGGGTTCAGCTTCTGCCGTGAGGATAATCCTACTCCGGAGCAGCTGGGCTCAACCATTGTGAGGGTGAAGAAGCTCTTCCCTGGGCAACCTGCTGCAGAGAGTGGGCAGATAGACATTGGGGACGTCATTCTCAAAGTGAATGGGGCATCGCTCAAGGGTTTATCCCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011078:ENSGALT00000018046:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.545 A=NA C2=0.194
Domain overlap (PFAM):
C1:
PF0059519=PDZ=PD(7.2=10.9)
A:
NA
C2:
PF0059519=PDZ=PU(77.9=93.1)
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:
AGCTTTCGGTGACAAAGGCTC
R:
ATAAACCCTTGAGCGATGCCC
Band lengths:
342-1163
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]