RnoINT0117110 @ rn6
Intron Retention
Gene
ENSRNOG00000021493 | Prdm9
Description
PR/SET domain 9 [Source:RGD Symbol;Acc:1305247]
Coordinates
chr1:57548963-57552331:-
Coord C1 exon
chr1:57552282-57552331
Coord A exon
chr1:57549120-57552281
Coord C2 exon
chr1:57548963-57549119
Length
3162 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
ATATGTGACTCTAATTAAAGGAA
3' ss Score
3.98
Exon sequences
Seq C1 exon
TCAGTTCTCCTTGGGTGCCTTTCCGGGTGAAGCACAGTAAACAACAGAAG
Seq A exon
GTAAGTGATTTCCAAAGCCTACAGACAAGAAAACCTTCCTCATGGATCCAAGCACAGGTAAGAAAAGGAAAAAGCTTAGAGTACTCTGGGAATTGCTACCTTCCCAGTCTCTTCTACACACTATCTCTCTTCCTCCCGGTCATTTGAATTAATAAGAACATCACTCACTTGAGTGTTCCTACCTCGGTTTTATTCTGCTATGTCAAAGGGAGAAATTTACTAATGTACTCTAAGGATAGTTTACGAATATACAGAGGATTTTTACTTTGGATGGCATGGATAAAGGAGATATGATCCTCTTCCTCATAAAGACTCATTCTGATAAGAAACAATAGCTCTCATCCCTAAGAAGATTCAAGTTTGATAGCAAGGGCTTCACAAATGAGAAAATGACTTAATCAGGCATGGTGGTGCTTGTCTGTAATTACATAGAATCAGAGTCCCAAGAAATACTGTGAGTTTGAGACCAGCCTAGTCTACTTAAGGAGTTCCAGGCCTGCCACAGGTATCCAGCATCATAGTGAGTTTTGGAATGGGGAAGAGAAAAGGATGTAAGATTTCAGATAGGCAAATAATTTCCATGGAAATGTCATCTGTGGGAGAGACTATAAAAGAAGCTAGTAATCTCACATTAATAATATATTCAATTGCACATGTTCTAGTCAGAATCACAAAAAGAATTATTATATGTGGGTGGTTGGAGAGAGGGCTCAGTGGTTAATAGCACTTCTTGTTCTTCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCACACACACACACACATACACACACATGAAAATAAATCTTTTTCTAAAAAAGATTTATTTATTTTATGTATGCGAACACACTGTCTCTCTCTTCAGACACACCAACAGAGGGCATCGGATCCCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATCGAACTCAGGACCTCTAGAAGAGCAGTCAGTGCTCTTAACCGCTGAGCCATCTCTCCAGCCCAGAAAATAAATCTTTAAAAATAAACAATTAGCATGTATATTTATGAAGAAAAATTAGTGAATTTTCTGGAAAAATTAGTACAAGAATTAGTTAATCTAATTCCAGAGTCATCCTAAGTATTGTGTAACTCAAGGACTTGAAGGGCTAAGGTAGGAGGAATCCTGTGAGTTTAAGGTCAGCCTCCATAATGAGACCCTGTTTCAAACAAGCAACCTAATTCTAGAATCAACTATTTCCAACATGCCAATTTACAATTTTAGCATCACTTTGTTAGTTGTAGCGGTACATTTCTACCACCATCTCTTCATTTTCTTCCCAGAGATACTGCTAAGCTCTCACTTCCTTTTACAGATGTGTGTTTAACTTTAACTTTGTTTTCTACATTTCTCATTTGATCACTATTTCCTACTTTGTAAATATAGTCTCTTTCTCTCTGTAAGCTTTATCTTCTTCATGGCAAGCTTTGCTGCCCTTCCAGGTACTCTTCCCAAATATCCCTGTCCCAAGCCTGAAAGAAGCCTGAAGGGAGAAAGCCTAGCATATGGCCTTGTGCGCTGAATTCATTTAAGTTCTTCCTCGTCTCTTTCTTATTCAGACACTCCACACATTAACTAAAGTCACGGGTGAAAATTTATAAAAAGCTTTAAAGAACTACAGAAATGCCTATTGTGGTTTTTATATGTGACTCTAATTAAAG
Seq C2 exon
GAAACACCCAGAATGCCATTAAGTGATAAATCTAGTGTGAAGGAAGTATTTGGAATAGAAAATTTGCTGAACACAAGTGGCTCAGAGCATGCCCAGAAACCAGTGTGCTCCCCTGAAGAAGGGAATACCTCCGGACAGCACTTTGGAAAAAAACTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000021493:ENSRNOT00000066370:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.647 A=NA C2=0.660
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF095145=SSXRD=PU(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
Mouse
(mm9)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]