RnoINT0122953 @ rn6
Intron Retention
Gene
ENSRNOG00000029001 | RT1-S2
Description
RT1 class Ib, locus S2 [Source:RGD Symbol;Acc:1595920]
Coordinates
chr20:3156874-3157073:+
Coord C1 exon
chr20:3156874-3156906
Coord A exon
chr20:3156907-3157029
Coord C2 exon
chr20:3157030-3157073
Length
123 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TCTTGCTTCTTCTACTGCAGGCA
3' ss Score
9.7
Exon sequences
Seq C1 exon
GTGGAAAAGGAGGGGACTATGCTCCAGCTCAAA
Seq A exon
GTAAGTGTGGGGGGCAGGAGTGTCTCTGAGGCTCTTGGGGTGAAGCTACAGCTCAGTCAGCCCATAATGGCCCCTCCATCCCCACCCGACATTCTCCCCAACGTCTTGCTTCTTCTACTGCAG
Seq C2 exon
GCAGCAACAATGTCCACCGGTCTGACTTGTCTCTGGAGGCTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000029001:ENSRNOT00000042882:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.857
Domain overlap (PFAM):
C1:
PF066797=DUF1180=PD(10.0=54.5),PF066236=MHC_I_C=FE(37.0=100)
A:
NA
C2:
PF066236=MHC_I_C=PD(48.1=86.7)
Main Inclusion Isoform:
NA
Other Inclusion 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:
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]