DreINT0114952 @ danRer10
Intron Retention
Gene
ENSDARG00000060184 | pkn1a
Description
protein kinase N1a [Source:ZFIN;Acc:ZDB-GENE-061207-17]
Coordinates
chr1:45129189-45131176:+
Coord C1 exon
chr1:45129189-45129298
Coord A exon
chr1:45129299-45131032
Coord C2 exon
chr1:45131033-45131176
Length
1734 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
GTGTATGTGTGTGTGCACAGTCC
3' ss Score
8
Exon sequences
Seq C1 exon
CGGATGTGAGCGCAGTATTGAAGCTGGACAACACTGTGGTGTGTCAGACGGCATGGAAGATGGTTGGAGAACAGGGCTGGGATCAGACCTTCATCATCGAGCTGGAGAGA
Seq A exon
GTGAGTTCAGCTCTGCGTTAATAGTAGATTTGCTCAGATTAGAGCTTCAGTATCTGTTTCATTAATTAACGCTCCAGGCATTAGACTGTAATTATAGTTATAAAAATAAAATCCTGCGGATATGTAACATCAGTGTCCCGCTAACTGGAGCGTCTCAAAAAACTCTTACGCAAGCAATGACAAGCTGTTGTTTAGGTTCAGAGGAAAAAAGCACACTGAACATGCAAAGTGATTAACGCTCATGCAAATTAAGACCGGCATGATTCAGCGACTCTTTTACAGTTATTTGTGTGTAATAAGTGGCAAGTGAATGTTTTAAAATATATCTGATCAGCATTTTAAACTAAAAACAAAAACTAAACCTATTTTTTTATTCAATAATTGAAACATTATTAGCTGTTTTATTACAGGGTCCCCGCAGAGTCTTAAAAAGTCTCTAAAATTTCTTTAATTTCAAAAACTAAATTTTAGGTCTTAAAAAGTCTTAAATTCATTAAAATGTTATCTAAACAGGTCTAAATTTTCCTCTGTCCAAGTAAAGCTACCCAGTGGGGCTGACATCCATCCAATCACCAACAATCCATCCTAATAAAACCTTATTTTTTATATTTAAGTTTTATATTTCAGTTTTTTAATGGCAAAGAGATAAAATTTGAAATAGTTGTTAGACATCTTTATAGCAATTTCTTCCAATTAAACTCCCAAATTTCCAATCACACAATTCCTAAGGATAATAACAGAGCAATGTGTCCCTTTACGTTATTTTCCATTCATAGAATTTTTTTTTTACAGGATTAGGAGGGAGTAGATATAATATTTCTATTATTTTTTATTAATTCCATTTCTATTAAATCCAACAAATGCATATTTTTGATCATATAACGAATACTTCACAATAAAAAATACTTTTGAACAATGTTAAACGTGTCATGTTGGAAAAAAGTGTATACAACTAGAGTTTTTTTGTTTGAACACATTAAAGTTGCTAAGAAGTAACAATAATAGTAATATGTTTGTGGCAATTAAAAAAGTCTAAAAATGTTATTCTTAATGGTCTTAAAAGAATCTTAAAATGTCTTAAATTTGACTTAATGAAACCTGCAGAAACCCTGTGTTTTTTTAAAAGGTCTTAAATTTCAAACACTAGTTTTAATAGTTCTTAATTTTCCTATGTCCATGTAAAGTTACCTAAAATTGTTTAAAGACCCATCCAATCACCAGCAATACATCTCTATAAAACTTCAAACAAAAGTTTATATATTAACTTTATTTACCAACATCATTTCATTATCTTCCTTAAAACAGCCGAGGCTCGAACCAGCGACCTTCTTGCTGTGAGACGAAAGTGCTACCCACTTTAAATACTTTTTAATAATAAAATATTTAAATATTTAATACAGCAAATATTATTAGTATAATGACTGTTTACTCTAATTGTTATAGCAAACTAACTAGCTGCATTGCTAAAAAATGAAATAAAATTCTGACAATGTGCTGTATACAAAATTGCCAAATCATAAAATGAAATGAAAAATGAATTAAAGCTAAGCAGAAATATTTAAAAACTTGTAAAAATGGCTCAAGTGCCGAACAAAATTGCTAACAAAAAAACCTGTAAATATAAATAAGCTCAAACAAAACAATAACACATTACGAAAAATATAAACGTAGTACTAGAATAAAGCTTTGATGTTGATGATATTGATTGATTTGTGTGTATGTGTGTGTGCACAG
Seq C2 exon
TCCAGAGAGATGGAGATTGCCGTGTACTGGAGAGACTACCGCTCTCTGTGTGCGCTGAAATTTCTCAAGCTGGAGGATTTCTTGGACAACCAGAAACACAAAGTACAACTAGAGCTAGAACCACAGGGACTGCTGCTGGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000060184:ENSDART00000132555:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGATGTGAGCGCAGTATTGA
R:
GCAGCAGTCCCTGTGGTTCTA
Band lengths:
246-1980
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]