RnoINT0122948 @ rn6
Intron Retention
Gene
ENSRNOG00000029386 | RT1-N2
Description
RT1 class Ib, locus N2 [Source:RGD Symbol;Acc:1595850]
Coordinates
chr20:3146856-3147456:+
Coord C1 exon
chr20:3146856-3147018
Coord A exon
chr20:3147019-3147186
Coord C2 exon
chr20:3147187-3147456
Length
168 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
TCACCATGCGCTAACCCTAGGCT
3' ss Score
6.78
Exon sequences
Seq C1 exon
AGTTGGGTTCTGAGATAATCCAATCCCTGTCGGTCTGGTTTATGAAGTTGTCCAAGATCAGCCCAGACCCATATGCTCTGGGTTCCCAAGGCTGGTGCGCTCTGGCTCAGTGCCCTTCTCCTGCTCCTGAATGCCTCCTTCTCCTGGACTTGGACCCCTGAGG
Seq A exon
GTGAGTGAGATGGGGGAGGGAAATTGCCTCTGCTGGGAAGGCCAGGAGTAGCACCACCCAGTCTCTCCTGTCCCCTTCTCAACCTGTCCGGATCCCAATCCAGGCAGCCTGCCCTGCTTCAAGCCTTCGCACCCGCCCAGTCTGGGTCTCACCATGCGCTAACCCTAG
Seq C2 exon
GCTCACACTCCCTGCGGTATTTCTCCATTGTCATGTCCTGGCTGGGCCTCCGGGAGCCACGGATCATAGTCAGCGGCTGCATAGATGATACGGAGTTCGTGCGCTTGGACACCAACAAGGAGATTGTAAGCCTGAAGCCCCTAGTGCCTTTGCAGGAGCAGGAGGGGCTAGAGTACTGGGAGCAGCAGGTTCATAAAGTCAAGACTCAAGAACAACAGTCTGCAAGGAACCTGATGATGCTGGTTCGTTTTTACAATAAGAGCATGGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000029386:ENSRNOT00000050159:1
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=0.000
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(0.1=0.0)
A:
NA
C2:
PF0012913=MHC_I=PU(52.6=98.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
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:
TTCTCCTGCTCCTGAATGCCT
R:
ATGAACCTGCTGCTCCCAGTA
Band lengths:
242-410
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]