DreINT0121944 @ danRer10
Intron Retention
Gene
ENSDARG00000103699 | ptpn13
Description
protein tyrosine phosphatase, non-receptor type 13 [Source:ZFIN;Acc:ZDB-GENE-070410-72]
Coordinates
chr21:9340636-9341882:-
Coord C1 exon
chr21:9341738-9341882
Coord A exon
chr21:9340851-9341737
Coord C2 exon
chr21:9340636-9340850
Length
887 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
CTGTTGTTTACCTGGTCTAGATA
3' ss Score
5.86
Exon sequences
Seq C1 exon
GTGGTGCATCTGTTGATGGAGAGAGGTCAGCCACCAAAAGACAGCATTCATGCTCCTCTCACTCCTCAAGGCACTTCAGAACCTCAGAACAAAACAGTGGAGGAGCCGTCAGCACCAGAAAAAGAGTACAACTTCATTACTGCAG
Seq A exon
GTATGAGCTGGAATATGCACCAACAAAGAAATGGAAATGCCATGATGCACATAATAGCTTAAAGGTCCCTTGAAGTGCTTTGAAATGTGCATTTTTTTATTCTATGTTTTAAGAGGCAAAAATTAAGAGAGGGTGGGACAAAGTAGCTCCTCCTATTTAAAAAAAAAAAAACAGCCAATATTTTTTTGTTTTTATCACAGCTCTACCAGTGAGAGTGGTTGAGCTCAAGCGCATCAAATTAAAAAAGCAAATGAGATGTGTCTTGAACGGAATGGGAAATATCAGTTACTAGAGAACTTTTGATTGGTTAGAAGATCTTTTGAGAGGTATGAGGTGACGAGAAAAAAAAAATCATTGATCCATTTGGGTGGAAGTGACAAACTGTCAGCTTTGGATGTTTATATCAGGTTTATATTTTAGAAATTCAAATTTTGTCATTGTTTTGGAACACACTAGCTTATAGATATCTTTAAGATGAACATACTGATACTAACATCTAATAAACGTTAATTTCACTGGACTTTTAAAAATGTGTTGTAAAAGAAAAAAAAGATCCCATTTAACAGCACTTGAGAAATATTTGAATTCAAATTGAACAAGGTTATTAATTTTGTCTGTATAATAAATATTGGAGATCCCTACCAGAAAGTATAAATATGTTTACCTTAACACATGGTGTGAAATAAGTGATTATTTCCAAATTATTTATTCCATTTTATTTATTTTATTTAGTTTTTCATAAGAGAAGTAACACTGATAAACACAGCTGACCTCTCACTTGTTGACTGCCAAATGAAATGTGCTAAAGGTACCGCAGAGGTGAACCGTGGGCTGGCATTTGAACTTTGGAAGAGTAAATGGGCATTTCTGTTGTTTACCTGGTCTAG
Seq C2 exon
ATAACACGTTTGATGTGGCTTTACTGAAGAACACGTCCGGCCTGGGCTTCAGCTTCAGCCGCGAGGAAATCATTCCCGGAGAGCCTCTGGGCTCCAGTATGGTCCGTGTCAAGAAGCTCTTTCCAGGCCAACCAGCAGCTGAAAGCGGACGCATCAAAGTAGGCGACGTCATTCTGAGGGTCAACCAGACGCCACTCAAGGGCCTGTCCCAACAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000103699:ENSDART00000162225:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.898 A=NA C2=0.306
Domain overlap (PFAM):
C1:
PF0059519=PDZ=PD(7.2=12.2)
A:
NA
C2:
PF0059519=PDZ=PU(78.8=93.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGATGGAGAGAGGTCAGCCA
R:
GGACAGGCCCTTGAGTGGC
Band lengths:
342-1229
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]