RnoINT0119977 @ rn6
Intron Retention
Gene
ENSRNOG00000002061 | Ptpn13
Description
protein tyrosine phosphatase, non-receptor type 13 [Source:RGD Symbol;Acc:1563360]
Coordinates
chr14:7731582-7733051:-
Coord C1 exon
chr14:7732594-7733051
Coord A exon
chr14:7731714-7732593
Coord C2 exon
chr14:7731582-7731713
Length
880 bp
Sequences
Splice sites
5' ss Seq
CAGGCATGG
5' ss Score
2.23
3' ss Seq
GTCTGTTTCTCTTCCTCAAGGAA
3' ss Score
8.11
Exon sequences
Seq C1 exon
TGCCTTCTACTCCTGTTCACTTTGCCAATGGAATGAAAAACTACACCAAGAAACCGTCCTCCATGCAGGACAGTGCTATGGACCCATCAGAGGACCAGCCCTGGCCACGGGGCCCTCTGAGGCACGTCCCAGAGAGTCCCTTTGGTCTCTCCTCGGGCCTGCGGGAAGGAAGCCTCAGTTCCCAAGATTCCAGGACTGAAAGTGCCAGCTTGTCCCAGAGCCACGTCAATGGCTTCTTTACCAGCCACTTAGGTGACCGAGGCTGGCAGGAGCCACAGCACAGCAGCCCATCACCACCTGTAACCTCCAAGATCACCGAGAAGACCTTCTCTGACAGTTACCGTAGCCCGGCCAGGCGGCAAGGCACCTGTGATGTGACTGAGCTCCCTGGCTGTGCCGACTCCGACATAGACGATCCCACTTACAGCAGCAGTCAAGACCGTCAGGCACCAAAACAG
Seq A exon
GCATGGCTTAACTCTAACCCGCTGTGTCTTCATTTCGCAGGGTAGACTCTGTTAGAGGCGGGTGGGACCCACTCAACTGCTCATGTGGCTGTAGGACAGAAGAACAGCTTGCATCTTCCTCTCTGAACTGCTGTCGCTGCTGCTGCATTTGCTGCTGACTGGCAGTCAAAGACCTTGAACACTGACCCTCAAGGGCTGTGCTCAGACGACGTCTCATCTCCAACACGTTCGAGCACGGGTCAGGGGAGAACTTGAATACCTGAAAACCTGTTCCTGCAGAGTTCATAGTGTGGGCAGTCTGATTTGCCGTGGCCCACCTGCATTCTTAAGGGGGAAAGCCTCTTTCTATCAGATAGGAACGTGAGCTCCCATTCAGAAACAGTTTCAGAGGGATGCGCACAGCAGAGCTCTCCTTCTTGGAGGCTGTGCAGTGGTCCTCACAGAAGCTCTCTGCCCTCGGGAAGAGCGCTTAGCTGATCTTTAAACCGCATTTGTACACATGAGCAGAGTGATCCCGAGGCTGGCTAGCTTAGACAGTCCAATTAGTCTGTTCCTCCGTACACACTGACCCCTAAAGAGAATGGGCATACGCCAAGCTCAGAAACAGGAAGCACAGGCAAAAGGCTCTTCCGAAGCTAAGTTCTGTTTCCCTCCACCTTGCCCAGCTTCACCTTCTGGGTGTCAGGTTCTAAACAATCGAATCAGTGTGCCCTGACCTGGCAGTGCCTGGAAAGTCTCCTGGCCTTCACGGTTTTGATATCCTCAATTCCTTAATACCTTGCTCTAGAAATTTTTTTTTTCCTGAAAAGTTTTGTTTCCACCGAGAGTTCGTTGGGCTCTAATGGGAAATCCTCCTGCCTGTCTGTTTCTCTTCCTCAAG
Seq C2 exon
GAACCTTCCTCCCCACTGAAAGCATCCGACAAAATGAGCTTTGCAGCCTTCCCTGGGCCATCCCCTGAGCCGGGAGACGCGTTTGAGGTCGAGCTGGCTAAAACCGATGGCAGCTTGGGGATAAGTGTCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000002061:ENSRNOT00000061162:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.955
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0059519=PDZ=PU(18.1=34.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTCCCTTTGGTCTCTCCTCG
R:
TTGTCGGATGCTTTCAGTGGG
Band lengths:
356-1236
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]