DreINT0114949 @ danRer10
Intron Retention
Gene
ENSDARG00000060184 | pkn1a
Description
protein kinase N1a [Source:ZFIN;Acc:ZDB-GENE-061207-17]
Coordinates
chr1:45120962-45123287:+
Coord C1 exon
chr1:45120962-45121080
Coord A exon
chr1:45121081-45123073
Coord C2 exon
chr1:45123074-45123287
Length
1993 bp
Sequences
Splice sites
5' ss Seq
AAAGTACAA
5' ss Score
-1.85
3' ss Seq
TCTCTCCTTTTCTTCTTCAGGCT
3' ss Score
11.91
Exon sequences
Seq C1 exon
GAAAGCCTGATCCATGTGGTATGGAGCTACGCATTGAAGAGCTCAGACACCATTACCGAGTAGAGCACGCCGTCGCTGAGGGAGCCAAAAACGTCCTTAGACTTCTTGGAGCCAGTAAA
Seq A exon
GTACAAGACAAGAAGGCCATGTCAGAGGTTAATTATCATATTATTACAATATGTAAAGATTCATTCATTCATTTTCTTGTCGGCTTAGTCCCTTTATTAATCCGGGGTCGCCACAGCGGAATGAACCGCCAACTTATCCAGCATGTTTTTACGCAGCGGATGCCCTTCCAGCCACAACCCATCTCTGGGAAACATACACACAAACACATACACACACACACTCATACACTACAGACAATTTAGCCTACCCAATTCACCTGTACCGCATGTCTTTGGACTGTGGGGGAAACCGGAGCACCCGGAGGAAATCCACGCGAACGCAGGGAGAACATGCAAACTTTACACGTCAACTGAGCTGAGGTTCGAACCAGCGACCTTCTTTCTGTGAGGTGACAGCACTACCTACTGTGCCACTGCTTTTTGTGTAGTTGCGGTCCTGCTGTGTAAAACATATATCCAGTATATGTTTTACACAGCAGATGCCTTTCCAGCTGCAACCCATCACTAGGAAACACCCATACACTCTCATTCACAGTCACACACATACACTGCAGACAATTTAGCTTACTAAATTTGTCTGTACTGCATGTCTTTTGACTGTGGGGGAAACCGGAGCACCTGAGGAAACCCCCGCCAACACGGGGAGAACATGCAAACTCCACACAGAAATGCCAACTGACCCAGCTGAGGCTTGAACCACCGACCTTCTTGCTGTGAGGCGATTGTGCTACACAACGCACTACCGTGACACCTAAATTTAAATTAAAATAATTTATTTTAGTTTAATTTATTTTTAATTTGTATTATTTTTTCATTTAATTTAATTTTACTTAAAATTATTTAATTTAAAATTATTTTATTTTATTTTGCCAAACTTTGACAATTAAGACATTTACCTTCACTTACTGGCATTTAATTTAATTTAATTTTACTCAAAATTATTTTAGTTTAAATTATTTCATTTTATTTTATTTAAAGTTATTTAATTTAAAATTATATATAAAAATATTTTATTTGCCCAACTTTGACAATTAGGACATTTGCCTTCACCTACTGGTATTCTATTTTATTATTTCATTTTATTTTTATTTTTTTTACTTAAAATTATTTAAATGAAAATTATTTTAGTTTATTTGGCCAACTTTAACATTTATGACATTTAACTCCACCTACTGGCAGTTTTGTTTTTGCTTTATATTAAAAAAAAAAGAAATTTAACAATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAAAATAAAATTATATAATATATATATTGTTACATTTTTTCCCAAAAATTATATACTTACCCTCATGATTTGGCAAACCTATTTGACCTTCTTTTACAAAACATTAAAGAGATATTTAAGAATGTTGGAACCCAAACTGTTTTGGGTACTGTTTACTGTCATTGCATGAACATAAATTACTAGGTCAATTTTTAAGATATTAATTATAATCCTTTCTTTTTTTTAAATTCAAGTTTTTTATTGTTTTCTTCTGGTTCATGACAAAATAATACAAACACATATTACAAGTGATCACTTGTGGCCTACTAAATGTAAAGCCAGAATGAATACAGTGGTTACTAGGACAAAAGTACAATATTATCAGGAGAACCTGGTGAGCAGTTTTAAATTGTGTTACAAGACATTATCACATAAGACCAAAAGTCTTCCCACACTGGGATACATACAGGGACCCCTGCTTTGTCCTTTTTATGTAATTTGTAAAGTAAACATTCATACGAGGCTGTTATAGTCATTATATTGACCCACTTGTAATCCTTTCTAAACTTTATGTTAAACTGTCTTAGTAATTATGCATAGTAAATGTTGAGTCAAATTTCTAGTATTAGTTTTGCCCTGTAGTATAGATCGTTTTGACTCTCTTTATATTTTCTTTCTCTCCTTTTCTTCTTCAG
Seq C2 exon
GCTCAGTGTCGTCTGAGTGAATCGTCGCAAAGGTTGGACCTGCTGCGAGATTCTTTAGATCGACGGTTAGCAGAGCTTCCTGAGGATCATCCCAAAGCTTCTGTTATCAAAGAGGAGCTGGTTTTAGCATCCTCACCAGCCTTCAGCTCTCAACACAGCGCCCCCTACCTGCACAACCAGTACAGCACTCTCTCCAAACCCTCACCCCTCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000060184:ENSDART00000132555:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.331 A=NA C2=0.222
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
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAAGCCTGATCCATGTGGTA
R:
GGGTGAGGGTTTGGAGAGAGT
Band lengths:
326-2319
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]