RnoALTA0032577-3/4 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000029386 | RT1-N2
Description
RT1 class Ib, locus N2 [Source:RGD Symbol;Acc:1595850]
Coordinates
chr20:3146856-3147311:+
Coord C1 exon
chr20:3146856-3147018
Coord A exon
chr20:3147187-3147255
Coord C2 exon
chr20:3147256-3147311
Length
69 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
GCTCACACTCCCTGCGGTATTTCTCCATTGTCATGTCCTGGCTGGGCCTCCGGGAGCCACGGATCATAG
Seq C2 exon
TCAGCGGCTGCATAGATGATACGGAGTTCGTGCGCTTGGACACCAACAAGGAGATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000029386-1-3,1-2,1-1,1-0-3/4
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
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 Skipping 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:
ATCCAATCCCTGTCGGTCTGG
R:
CCGTATCATCTATGCAGCCGC
Band lengths:
170-239
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]