DreINT0016697 @ danRer10
Intron Retention
Gene
ENSDARG00000101293 | PKN2 (1 of 2)
Description
protein kinase N2 [Source:HGNC Symbol;Acc:HGNC:9406]
Coordinates
chr6:25349510-25351651:-
Coord C1 exon
chr6:25351497-25351651
Coord A exon
chr6:25349724-25351496
Coord C2 exon
chr6:25349510-25349723
Length
1773 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGT
5' ss Score
7.7
3' ss Seq
ATTCAATCTTTGTCTTGCAGGCT
3' ss Score
8.51
Exon sequences
Seq C1 exon
TGACTACAAGCAAGCCCATCATCAGCCCTCTGGACCTGAGGATAGAGGAGCTGCGACATCACTACCGGATAGAGTCTGCTGTGGCCGATGGTGCCAAAAATGTGATGAAGCTATTGGGAACAGGAAAGGTGACAGAGAAGAAAGCTCATTCTGAG
Seq A exon
GTCAGTCTAAATCCTCATAGTTTTTATATAGTGTTCTCTGCATATGCTTTCATGCCTGTATAGCTGTTTAATCCAGTTACTCATTTAACTGTTTGCTTGTAACAGCTTTTGTTGCCTGAAGCAGCAGATGTTTACAGCTTTTCTCATTGTGTATCATATTAATTGTGCTATGACACAGAATGCTTAAATGTTCTTTCTTATGTAATTGTTTTATAATTGTGAGAGTAATACAGTTTTTTATACAGCGGTTTATATTAAAATGTGTTTAAATTATTTAGTTTTGGGATGCAACAGTGAAAATATCTGTCCTACGTGACAGAAACCTTTTTTTTTTTTTTTTGTTGGTTAGAAAATCTATATACAGGGTGAAAATGCTGGCAACACATGATAGCAGTAAATTAGACAGCTGCTGAATCACTGCATATTTGGGTTTGTTCCTATTGCACAACTGGTAGAACAAGGAAAAAAAAAAGTCTTGTTTGATTTTGTGGGATAGAGCGTCTGCACAGAATATGAATTAAAACAATAAAAAAAATCTATAGATATTATAGTATTTTTGGAGGGGGTACTTAGCTGTACATTTTCAAATTGATGTAAAATGCTTGCATTCTTAACTTATTGGAAATAAAATAAGCTACAATCATACTGTTTACAGGCATACAGAAAGACAGAAATAAATGTTGAGTATATAAGAATAGTGGATATGTGACTTCCGAGAGAAAACAGTTTGTTTTGTTTTATTTTCACTTGTAAATTCAAAAAGACCTGTTAACACATTGGATTTAATATGAACTCTTGACGTAGAAAGACCTCAATAGTATTTATTTATTTATTTTTTATGTAAAACACAACACAGTAATGTTTTGTTTTCAGCTAAAATACAAGTGTTGTGTTAACCATTAATTTCTGTGCTTTATTTTTAATTAAACATATAAATGAGTTAATATCATGAATTAATAAAATGAATGAATAATCTTAATTTTGCTTTTAAATGTTGTTAGACTAGTCAAAAATAATTCCGAATTGCATACATGAGTGTGTTCTAGAAATAAACCAAGAAAGAATTTGTTATAACAGCATTTGTTACCAGATAAATTTGAATCCCTGATCTCTGAGGCTCTCAAGTTGATGATGAGTGTGTTAAACTGTGGCATACATCCATACATATATGTACTACTGTGTTTCTCCATTACAGTTTCCAAACCTTTACTTTTAAAGCATTTCTTTGGAGGTTTTGCATCCATCTGTATCCAGATTTGCAGTGCTCAGCATAATTGATTACACCCCATTTTGAAAATCAATATTTTTATCTATTTCTCAGTGAATATAAGCAATGTATTTTGGTGGATTTAAACAAAACCGATTTATTAAACAGAAATATTGATTAACATAATACTTTAATCACCAAACATATTTAGAAATTGAAAGATAAACAATTAAATTCAAGCTAAATATTGCAAAAAAATTTAATTACAACCTACAAAATTTCAACAAAAACTAAAATTTCCCTTTTTTATTTTGTATTTAATATTTTTCTATAACATACATTTGGGTGTGCTAGTTTGTTGAACATTATCGTAAGTGGTTTTGTTGGATAAGCTCCAGATTTTTCTTCAGTACTGACTAATCTTATGTATATGCACAGATATAATATTGTATAGCTTCCTATTAAAAATATCAATTTAAAAGATAGATTTTTTTTGTTGTGTACTTGCATATGCTGAGCACTGTCTGTCTGTATAATTTTGTAAGCATTCAATCTTTGTCTTGCAG
Seq C2 exon
GCTCAAGCCCGCTTGAATGAGTCTAGTCAGAAGCTGGACTTGCTGAAGTTTTCTCTGGAGCAGAGGCTCAGCGAACTGCCCAAAAATCACCCAAAGGGCACCCTGATCATGGAGGAGTTAGCAATGGTGGCCTCCCCTCCTAACAGTCCCCGCCAAAGCATCATGTCCACCAGCAACCAGTACAGCACTGTGGCCAAACCTGCTGCCCTGACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000101293:ENSDART00000169030:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.269 A=NA C2=0.568
Domain overlap (PFAM):
C1:
PF154561=Uds1=FE(57.3=100),PF0218511=HR1=PU(53.4=75.0)
A:
NA
C2:
PF154561=Uds1=PD(33.3=40.3),PF0218511=HR1=PD(43.8=44.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAAGCAAGCCCATCATCAGC
R:
GTTTGGCCACAGTGCTGTACT
Band lengths:
349-2122
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]