DreINT0121938 @ danRer10
Intron Retention
Gene
ENSDARG00000103699 | ptpn13
Description
protein tyrosine phosphatase, non-receptor type 13 [Source:ZFIN;Acc:ZDB-GENE-070410-72]
Coordinates
chr21:9356582-9357725:-
Coord C1 exon
chr21:9357618-9357725
Coord A exon
chr21:9356714-9357617
Coord C2 exon
chr21:9356582-9356713
Length
904 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
CATTTCGGCTTTTGCTACAGGTG
3' ss Score
9.43
Exon sequences
Seq C1 exon
GTTTTCAGGTTGTTGGAGGAGAGAGTTCAGGCCGTCAGGACCTCGGCACCTTCATCAGCTCAATCACACCTGGCGGACCAGCAGACCTCAACGGCTTGCTGAAACCAG
Seq A exon
GTATGAAAAAAACCCTGTATTTTAAACTCTTTATTCTGTATTTTGTATTTAGCAAGTCACATCAATTGATAGAATTTGTAGGAACTTATTCCTTAAATATCCAAAGCACTATAATAAACATTTTGCATCCGCATATCAAAGCAAATTATGATCTTATTTTGTGCATGCTTTACATTTAAATAGTATTAGAGGCCCCTAGGGGGCATTAGCAACTTACAAATAGGGATGTAGAATGACTTGAATTGGGTGCAGTAGTGTGTCTTTGTCTATGTACAGTGTGTATGTATACACTCCACAAATATATAAACACAACACTTTCACAATTTCTATGTACACACACACACACACAAAAAAAAACGAATTCTCTCAAATATTGTTTACACATTAAAAACCAGTGTTCACACACACTCATTGTTGAGTTAAAGGCATAATTTACCCAAAATGAAATGAACTCTGTTTACTCTCCCCCAAGTGCTTCCAAACATTGATGAGTTTCTGTTTTCTAAACACAAAAGAAGATATTTTAAAGAAAGATGAAAACCTGTAACCATTGACTTCCACGGTGGGAAAAACAAATACTGTGGAAATTAATGGTGACAGGTTTCCAACATTCTTTAAAACATCTTTTTGTGTGCTCAACAAAAGAAAGTTTAAACAGGTTTGGAACAAGTGAAGGCTGAGTAAATGATGGACAGAATTGTCCGTTTTGGTTGAACTATTAACTTTAAGTCTAACAGTAAGTTGTAGTACAATTAATTTCAAGTTATACTTTTTTATTATTATTAATGTTTTAGGTTTGAAGTAATGATATCTCTGTCCCAGGACATTTGTTTTGTCCCTCGATTGTACAATATAAGCTTATGTGTAATCTTCAGTGTAAGCTACATTTCGGCTTTTGCTACAG
Seq C2 exon
GTGACAGACTGTTAAGCGTGAATGATGTCAGTCTGGAAAGCCTCTCTCACACTACTGTGGTGGAGATGCTGCAAAGCGCCCCTGATGATGTCTCACTGGTGGTCTCTCAGCCAAAGGAGAGACTGTTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000103699:ENSDART00000162225:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.600 A=NA C2=0.624
Domain overlap (PFAM):
C1:
PF0059519=PDZ=FE(42.9=100)
A:
NA
C2:
PF0059519=PDZ=PD(41.7=77.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTTTCAGGTTGTTGGAGGAGAGA
R:
TGGAAACAGTCTCTCCTTTGGC
Band lengths:
239-1143
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]