RnoINT0119978 @ rn6
Intron Retention
Gene
ENSRNOG00000002061 | Ptpn13
Description
protein tyrosine phosphatase, non-receptor type 13 [Source:RGD Symbol;Acc:1563360]
Coordinates
chr14:7730115-7731713:-
Coord C1 exon
chr14:7731582-7731713
Coord A exon
chr14:7730209-7731581
Coord C2 exon
chr14:7730115-7730208
Length
1373 bp
Sequences
Splice sites
5' ss Seq
ACGGTACTG
5' ss Score
5.88
3' ss Seq
GCTCTGTCTGTTCCATTTAGGGA
3' ss Score
9.32
Exon sequences
Seq C1 exon
GAACCTTCCTCCCCACTGAAAGCATCCGACAAAATGAGCTTTGCAGCCTTCCCTGGGCCATCCCCTGAGCCGGGAGACGCGTTTGAGGTCGAGCTGGCTAAAACCGATGGCAGCTTGGGGATAAGTGTCACG
Seq A exon
GTACTGTTTGACAAGGTTCCACACCTTCTCTTCTTCACCCCCAGTAGACCGCTGTAGCCCAACCCGTTAGATGAGTCATGGTGACATGGATGGGACGCTTGCCAAATGCTTCCAAGAGCTAGAAATCGACAATCTTGAAAACTCGCTTAAAATTTGTTCACTATTCACCCACCCCCCTGTGGTTTTAAAAAATTTGGGAATTGCCTGTTCTCCATACATTTCATACTTGCTTAATTTAAGCATATCATATGCAGAATATGCAGTGTATGGCTACTTTTTGTATATATCTAATGGTTTCTGCACGTGTAAAATCGTGAGATGATAATCTCTTTAGCCCATGAATAATTAAAGAACGTGAATATTTACGTGCTAGTTCTCTAATACACATTCCCTGGTAACACATTTAAAACCTTAAAAGTAGAGGTTCCAAAACTGCCCACATACCTTTAAGATAACAGAGATATGAATATAAACTACTCGATAACATTATCTTAGAATTCTATAATGCGTTATTCCAGAACTGCAGCTTTATCAGTTGTCACAGTCTAAGGTCCCTCCCTGGTCATTGCATAAGCAATTAAAGGTGGAGGTAAGCCAGCGCGGGAGATGAGTCAGGGGGTTCAGGTACCAACACCCACATTAAAAACAAACCAAACAGGATACACAGTGCACGGGGCAGCCCTGCACTGGGGTGACACAAGGCTTCCAGGGATTGCTGATCATCCAGTCCAGCCCAGACAGCAGGCTAGGTGTTGAGAGACAGACCCTACCTCCAAAATCAGAGAAGCAGTTAAAGAAGACTCCTGCATCAGCCTCTAGACTGGCGTGCACACGCACATGCACACATACAGAACCTTTTTGCCAAAGCCTTCTCTTCTGTTTTTATTTTGTTTGTTAGTTTTTTGTTTTCTTTTGTTGTGTTTTTTTGAGACAAAGTCTGTCCACGTATCCCTTCCTGGCCTGCAACTCACAGAGATCCACCTGCCTCTGTCTCGTGCTTGGACTAAAGGTGTACTCCACCATTCTCAGCCTCCTTTAACATAAAAGAAAAGCGGCGTTAGTCCCGCACAGGTGAACATTGCTGTCTGCTTGGCTCGCACTGCGGGGCACAGAAAGGGACAGCAGTTCCCTACTAGCCAAGATGTGGCTTACTGATCCAGTGAACAGGAGAGACAGACAGAGAGGCAGAGAGGGGAAACAAAACAGCAAACTGCCTTCCATGTGGGGATGCAGTTAACAGTGCTGCTGGGCATTAACTGAGCAGCTGATGTGGAGTCAGCTCTCTCTGGGAATCGAACCCTCTCTAGCGCTCGCCTTTGAAAGCGTGCAAATACTTTCATGTCAATCCTTGCCGCTCTGTCTGTTCCATTTAG
Seq C2 exon
GGAGGTGTGAATACCAGCGTCCGGCATGGTGGTATCTATGTGAAAGCCGTTATTCCCAACGGAGCGGCAGAGACAGATGGCAGAATTCACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000002061:ENSRNOT00000061162:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.955 A=NA C2=0.656
Domain overlap (PFAM):
C1:
PF0059519=PDZ=PU(18.1=34.1)
A:
NA
C2:
PF0059519=PDZ=FE(37.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACCTTCCTCCCCACTGAAA
R:
TGTGAATTCTGCCATCTGTCTCTG
Band lengths:
223-1596
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]