RnoINT0117108 @ rn6
Intron Retention
Gene
ENSRNOG00000021493 | Prdm9
Description
PR/SET domain 9 [Source:RGD Symbol;Acc:1305247]
Coordinates
chr1:57553108-57553665:-
Coord C1 exon
chr1:57553542-57553665
Coord A exon
chr1:57553216-57553541
Coord C2 exon
chr1:57553108-57553215
Length
326 bp
Sequences
Splice sites
5' ss Seq
TAGGTAACA
5' ss Score
6.25
3' ss Seq
AACATCTTGCTTCTTTTCAGGTC
3' ss Score
10.83
Exon sequences
Seq C1 exon
GTCAAAGATGAGTTCAAAGACATTTCCATATACTTCTCCAAAGAAGAATGGGCAGAGATGGGAGAGTGGGAGAAAATTCGCTATAGAAATGTGAAAAGGAACTATAAAATGCTGATTTCTATAG
Seq A exon
GTAACAAGAAGTCTTGGGTTGAACCAACCTAGATAAAAAACAAGTCTCCAATTCCCTTGTTATGTTAGTGCTGTCTCAGGTATCTAGAGTGGTACAGTTCCCAATGGAGACAAGTTTAGAAGAAATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATCTCATTTCCACACCAAGAGCCTACCTGGCCTTGTGATACTTTTCGTCCCATCCTCCAGGACCTGCTTCATTTTTTAAGAGGAACATCTTGCTTCTTTTCAG
Seq C2 exon
GTCTCAGAGCCCCTAGACCAGCTTTCATGTGTTACCAAAGGCAGGCAATCAAGCCCCAGATAAATGACAATGAGGATTCTGATGAGGAATGGACACCAAAGCAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000021493:ENSRNOT00000066370:3
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=0.568
Domain overlap (PFAM):
C1:
PF0135222=KRAB=WD(100=92.9)
A:
NA
C2:
PF0135222=KRAB=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAAGATGAGTTCAAAGACATTTCCA
R:
CTTGCTGCTTTGGTGTCCATT
Band lengths:
230-556
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]