DreINT0114978 @ danRer10
Intron Retention
Gene
ENSDARG00000101983 | pkn2
Description
protein kinase N2 [Source:ZFIN;Acc:ZDB-GENE-061207-42]
Coordinates
chr2:22808942-22809469:+
Coord C1 exon
chr2:22808942-22809059
Coord A exon
chr2:22809060-22809332
Coord C2 exon
chr2:22809333-22809469
Length
273 bp
Sequences
Splice sites
5' ss Seq
AGGGTAACA
5' ss Score
4.9
3' ss Seq
TTTTTTATTTTTGTGTACAGGGC
3' ss Score
9.31
Exon sequences
Seq C1 exon
TGACCCAATAGTGACAAAACTGGACTTTGACAGAGACACTACACCAAAGAATTACTCTCCTGTTAGTGTGCGAGAAGTCCTGCCCGAGGACAAGATCTCCAACAAAGAGCGAGAGAGG
Seq A exon
GTAACATCACACTATCATGCGGTTACTATCGAGATAAACATTGATGCCATCTGTTTCCTTGAAAGCACTTTTTTAAACTCTGAGGATAAAGATCTGAAGCAGACACATAACTCATGCTCAGTCTCTCATCTGCCCCCTTGCATATAAAAGGAAAAGGAAATGCCTTCACGTTACCTTTATTAACGGAAAGATAACCGCTATCCACTCTCATCTTGTGTAAACAGTGGCAGCTGAAAGACTGTTGTTGTTGATGTTTTTTATTTTTGTGTACAG
Seq C2 exon
GGCGCTTTGACTGCGTTTGCCTACCGAAATGACAGGAATAGCATCATTGTACAGTCTGGCCTTGAAGAAATAGTTGAACATGACACTCCACCTTCAGCATTACAGCTCATAAATGTCCAGAAAAGCACAGAAATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000101983:ENSDART00000172715:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.625 A=NA C2=0.261
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGACCCAATAGTGACAAAACTGGA
R:
ATTTCTGTGCTTTTCTGGACATT
Band lengths:
252-525
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]