GgaINT0071084 @ galGal3
Intron Retention
Gene
ENSGALG00000011078 | PTPN13
Description
NA
Coordinates
chr4:47293201-47294527:-
Coord C1 exon
chr4:47294353-47294527
Coord A exon
chr4:47293355-47294352
Coord C2 exon
chr4:47293201-47293354
Length
998 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
TTCTTCAATGTTCATGGCAGACA
3' ss Score
5.83
Exon sequences
Seq C1 exon
ACGAAGAAAGGGAAGAATGATGATACAAGGAGGAAAGTCAGTGTGATGCTTCTAAGTGGACAGAAGCTGGAGCTGACCTGTGACACCAAAACAGTTTGCAAAGATGTCTTTGATATGGTTGTTGCCCATATTGGCTTAGTGGAGCATCACTTATTTGGACTGGCTAGTTTAAGAG
Seq A exon
GTAAGAATAAAAATTTTCTGGAGCAGATAGGTATAGAACAACGAGAGCTAACTACAGGATGTTGGGAATAATTGGAGGCTGCCTGGCATGTGCTTTGATGTCACATTGAGTTACACGCTCTTGTATTAGGCAAAATGCGTTCTTCAGGGAAGAAAATGTTTACTCAACAAAAGCCTGCATTTGTCTGAGTAGCAGCATCTCAGCTAGTTCTTTTTGGTTGCTGAGTGTTCTTCACTACTGCTTGTTGCCTTCACGTGTGTTGCTGTCTAGTGCCACACAGAAGATGTGAGCTGGGTTTTCTTGGTATGTTCTCGCAGCCTTTTCGGGGCAGCCCACAGGTATGCTGGGGCAAATGGTAGGGCCTCTTGTACAGAGTACATTGCCTTCAGACTAAATGAATTTATTTCTGAACTGTTCATTTTCTGCTGTTAGAACAGACCAGATGTTGGACTTCACTTTCCCCAAAGGGGAGAAGATCACTTTGGCAGCACTTACATATTGAGACCCACGTTTCCTGTTTTTGTGTCTAGCAGGATATCACAGAGCTGTAGCACTCAGAGTTCTGGCATGAGTCAGAAAACCTGAGCAGCCTGAGAGCCTTCTTCATCTGTGCTTGGCTCCCAGTGCCTTTGACAATTCAGCCATGAAAACGTTCTGTAGAAGTGTAAATTGGACATAAATAGTAAGGGAGGGAGGGAGTGGCAGATTAGGAATTAAGAAATTTGAGGGATACCGTGGTGCCTGATTCATAGCTATCATGGAATATGGTTTTTCTTTTTCTGCTCTCGTATTTTTTTGTTAACTAAAAAAGTATTTCTACTGCTATTGCTCAGTGTTCCCTTCAATAGCCATTGTGCTTACAAGCCATTGTTAGGACAGTAAGGTTTTCTTATGGCTGAACTGAATTCCAGAATTGGAAATCCAGTCCTGATCCTCCGGCTGGAAAAACGACTTCGTTCTGTTTTTACCCATGTCCTTTTCTTCAATGTTCATGGCAG
Seq C2 exon
ACAATGAATTTTTCTTCGTTGATCCTGACATAAAGCTGAGCAAAGTAGCTCCAGAAGGATGGAAAGAAGAGTCGAAGAAAAAGAACAAGCCCCCTGTCAACTTCACGCTGTTTTTTCGCATCAAGTTTTTTGTGGATGATGTCAGTCTTATACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011078:ENSGALT00000018046:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.034 A=NA C2=0.038
Domain overlap (PFAM):
C1:
PF093795=FERM_N=PU(49.4=74.6)
A:
NA
C2:
PF093795=FERM_N=PD(49.4=84.6),PF0037313=FERM_M=PU(5.1=11.5)
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:
ACGAAGAAAGGGAAGAATGATGA
R:
TGTATAAGACTGACATCATCCACA
Band lengths:
329-1327
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]