RnoINT0117113 @ rn6
Intron Retention
Gene
ENSRNOG00000021493 | Prdm9
Description
PR/SET domain 9 [Source:RGD Symbol;Acc:1305247]
Coordinates
chr1:57546915-57547616:-
Coord C1 exon
chr1:57547345-57547616
Coord A exon
chr1:57546983-57547344
Coord C2 exon
chr1:57546915-57546982
Length
362 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
TATTTTTTTCTGAAACTTAGATC
3' ss Score
5.67
Exon sequences
Seq C1 exon
ATTGTGAGAAGTGCCAGAATTTCTTCATCGACAGTTGTCCCAACCATGGGCCTCCTGTATTTGTAAAAGACAGTGTGGTGGACAGGGGGCATCCCAACCACTCAGTCCTCAGTCTGCCCCCTGGGCTGAGAATTGGTCCATCAGGCATCCCTGAAGCTGGACTTGGAGTATGGAATGAAGCATCTGATCTACCAGTGGGTCTGCACTTTGGTCCCTATAAGGGCCAGATTACAGAGGATGAAGAGGCAGCCAACAGTGGATACTCCTGGCTG
Seq A exon
GTGAGAAATGCCTTCTTTCCCTTCATCCTCTGTCTCCCCCCTTCCTTTTTGTGCTTCTGGTGTGACAAACTAGGATATGGACAGGGACAACATGACTAATTGTGTGTACTGAATGGTCTTTGTACAACATGGGTGGGAGTCCCGCTTCAAGATCTGAAGGTAAGTAGGGTTAGCCACTTTCAGGCTAGCGGTAGTGGTCCAGAGACAAAGAAAGCACACGTGTACATGATGACTCAGAAGCCTCATGTGTGGTCACTGTGAGTGGCTGAGTCCAACACTCAGGGAGCACTGGTGAGTGTGCAGTGACATGATTTCATTATTGTCATTCCCAGAGTCTTAATGTATTTTTTTCTGAAACTTAG
Seq C2 exon
ATCACCAAGGGAAGAAACTGCTATGAGTATGTGGATGGGCAGGATGAGTCCCAAGCCAACTGGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000021493:ENSRNOT00000066370:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.154 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0085623=SET=PU(21.7=19.8)
A:
NA
C2:
PF0085623=SET=FE(26.5=100)
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGAGAAGTGCCAGAATTTCTTCA
R:
CATCCAGTTGGCTTGGGACTC
Band lengths:
336-698
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]