RnoINT0112253 @ rn6
Intron Retention
Gene
ENSRNOG00000004131 | Pkn1
Description
protein kinase N1 [Source:RGD Symbol;Acc:69308]
Coordinates
chr19:24818139-24818879:-
Coord C1 exon
chr19:24818734-24818879
Coord A exon
chr19:24818353-24818733
Coord C2 exon
chr19:24818139-24818352
Length
381 bp
Sequences
Splice sites
5' ss Seq
GAGGTGACA
5' ss Score
3.85
3' ss Seq
TCTCTGCCTTCCTACCTCAGGCT
3' ss Score
9.52
Exon sequences
Seq C1 exon
GAGATCCAGACCTGGGAGCCGTAGAGCTACGCATTGAGGAGCTACGACACCATTTTCGAGTAGAGCATGCAGTGGCAGAAGGCGCCAAGAATGTCCTGCGTCTGCTCAGTGCTGCAAAGGCCCCAGACCGCAAAGCAGTCAGCGAG
Seq A exon
GTGACATTGAGGGCTTCTGCTGGAGGCGTGGCATTCAAGGGATGTAAAAGAGAGAGGTCCTGGTGAGGGTGGCACAATAACTCAGGTGGACTGCCACTGGGTGTGAGCCTCAGTAGAGAGGAGGACAGCATTAGTCCTGTCTATGCTAGAGCTTCAGGGGGAGGTGAGGCCTGCGAGAGGTCCTCACAACAAGAAGCTTTAATGTGGGTGGTACCTCAGGGGGTCCTGGCACCAGCGAGGGGCAAAGCCTAGTTTTCAAGGTTCCACCTGATGGGTCTAAGTAGGTTTGAGGTTTAACCTTGAGGAAGAAGTTGCTAGAAGTGGGTGGGTTCTTGGGGAAGGGCCTATGCCTGTTCTCAGCTCTCTGCCTTCCTACCTCAG
Seq C2 exon
GCTCAGGAGAAATTGACTGAGTCCAACCAGAAGCTGGGCTTGCTGCGGGAGTCACTGGAGAGGCGCTTGGGGGAACTGCCTGCTGATCACCCCAAGGGACGCCTGCTTCGGGAGGAGCTCACTGCGGCCTCATCGGCAGCCTTCAGTGCAATACTGCCTGGGCCCTTCCCTGCCACTCACTACAGCACCTTGAGCAAGCCTGCACCACTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004131:ENSRNOT00000005770:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.265 A=NA C2=0.551
Domain overlap (PFAM):
C1:
PF0218511=HR1=PU(53.4=79.6)
A:
NA
C2:
PF0218511=HR1=PD(43.8=44.4)
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:
CAGACCTGGGAGCCGTAGAG
R:
CTGTGAGTGGTGCAGGCTTG
Band lengths:
354-735
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]