RnoINT0117111 @ rn6
Intron Retention
Gene
ENSRNOG00000021493 | Prdm9
Description
PR/SET domain 9 [Source:RGD Symbol;Acc:1305247]
Coordinates
chr1:57547823-57549119:-
Coord C1 exon
chr1:57548963-57549119
Coord A exon
chr1:57547925-57548962
Coord C2 exon
chr1:57547823-57547924
Length
1038 bp
Sequences
Splice sites
5' ss Seq
TGAGTAAGA
5' ss Score
5.11
3' ss Seq
ACCTTTGTTCTCCAATCCAGAAC
3' ss Score
9.59
Exon sequences
Seq C1 exon
GAAACACCCAGAATGCCATTAAGTGATAAATCTAGTGTGAAGGAAGTATTTGGAATAGAAAATTTGCTGAACACAAGTGGCTCAGAGCATGCCCAGAAACCAGTGTGCTCCCCTGAAGAAGGGAATACCTCCGGACAGCACTTTGGAAAAAAACTGA
Seq A exon
GTAAGAATAAATAATTTGGGAACTTAAATCCTCTAGATTACCTAGGAAGGTTAATGGGAATGGTCTGGAATGGTCAGTGTAGTAACTTTAAAGAGTTCTAAACTTGGTCTTGTCTAAGCTGTGGCATTGGTTGTGGGCATGCTACTAAGTAGTATGTTGGAACACTGACTTTAAAGGCACGCACTTGGGTTGTTATTTGCATGGAGGTGCTGGGACTTGGGCAAGCTCTGTGACCTTGTGAAAGTTAATATGTGGAAATAAGGATATGGTAGCTCTGTGTTGCTCTCAAACAGCAAGTGGAGCATAAAGTAACGGGTCCAATAAATCTCTGCGGCAATAGGAGCCAAATACTCTCAGTGCTGTTTGCCCAGGCCTTTGCTCAATGCCCAATTGCCGTGTGCCCTTACAAATATTTTACAAATGAATCAACATGTGAATGGACCTTTTTAAATAGAAAATGTGGGTAAGTAGAAATTAAACCCGAAGAGTCGGAAATTAAAATTCGATTAGACATCTGTTGTCAGATAAATGTGAGATTTTAGCTTCTTTAAACACAAAGTTAAAGGGGGAGCATATGGCAGTAAATTCCACATTCTTTTTAAACATTTTAAAATATATTTTAGATTTTTAAAGATTTATTTTGGGGTTGGGGATTTAGCTCAGTGGTAGAGTGCTTGCCTAGGAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCGAAAAAAAGAACCAAAAAAAAAATAATAAAGATTTATTTTCACACGCATGTGGATGTCTGCCTCCACGCATATATGTGTACTATGTACAAGCCTGATGCCTGCAGAGATGGGATGGGAGTATTTGATTACCTAGAACTGGAGATACAGATGGTTGTGGGCCACGGTGTGAGTGCTGGGAACCAGACCCAGGCCCTTTATAAGAACAGCGTGTGCTTTAGCTGTTGAACTAGTTCCCCAGGCCTAGAGTTTAGATTTTATGAAGAAACAGGGATAAATGCTCAAAATTCACATACTTCAAGTCACCTTTGTTCTCCAATCCAG
Seq C2 exon
AACTCAGGAGAAAGAATGTTGAAGTGAATAGGTACAGGCTGCGAGAGAGAAAGGACCTTGCATATGAAGAGGTCAGCGAGCCCCAGGATGATGACTACCTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000021493:ENSRNOT00000066370:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.660 A=NA C2=0.143
Domain overlap (PFAM):
C1:
PF095145=SSXRD=PU(0.1=0.0)
A:
NA
C2:
PF095145=SSXRD=WD(100=94.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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:
ACACCCAGAATGCCATTAAGTGA
R:
AGGTAGTCATCATCCTGGGGC
Band lengths:
254-1292
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]