RnoINT0122902 @ rn6
Intron Retention
Gene
ENSRNOG00000031090 | RT1-CE7
Description
RT1 class I, locus CE7 [Source:RGD Symbol;Acc:1595786]
Coordinates
chr20:4698167-4698718:-
Coord C1 exon
chr20:4698640-4698718
Coord A exon
chr20:4698437-4698639
Coord C2 exon
chr20:4698167-4698436
Length
203 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
CACCGCGCCCCCCCCCCCAGGCT
3' ss Score
8.82
Exon sequences
Seq C1 exon
TCTCAGATGGGGTCAAGGGCACCTCACACTCTGCTTCTGCTGCTGGCGGCCGCCCTGGCCCGGACCCAGCCCCGCGCGG
Seq A exon
GTGAGTGCGGGGTCCGGAGGGAAACGGCCTCTGCGGGGCGAGGCGCGGGCGGCACCGCGGAAGCCGGGTCACCGCGTCGCACACCAGACCCCCGCCCCTTCTCCACCCGCGTCCCGAACCCGGCGCCCTGCTCCCCGCCCGGCCCGCGCACCCGCCCAGGATCCTGGGAGGAGGTCGGGGTCTCACCGCGCCCCCCCCCCCAG
Seq C2 exon
GCTCGCACTCGCTGCGGTATTTCACCACGGCGCTGTCCCGGCCCGGCCTCGGGGAGCCCCGGTTCATCTCTGTCGGCTACGTGGACGACACGGAGTTCGTGCGCTTCGACAGCGACGCGGAGAATCCGAGATACGAGCCGCGGGCGCCGTGGATGGAGCGGGAGGGGCTGGAGTATTGGGAGCAGCAGACACGGAGAGCCAAGGGCAACCAGCAGACTTTCCAAGTGAACCTGAGGACCGCGCTCCACTACTACAACCAGAGCGAGGACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031090:ENSRNOT00000047527:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.165
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(0.1=0.0)
A:
NA
C2:
PF0012913=MHC_I=PU(50.3=98.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCACACTCTGCTTCTGCTG
R:
CGGTCCTCAGGTTCACTTGGA
Band lengths:
298-501
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]