RnoALTA0032580-2/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000029001 | RT1-S2
Description
RT1 class Ib, locus S2 [Source:RGD Symbol;Acc:1595920]
Coordinates
chr20:3156578-3156906:+
Coord C1 exon
chr20:3156578-3156694
Coord A exon
chr20:3156859-3156873
Coord C2 exon
chr20:3156874-3156906
Length
15 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
TCTCCCTTTAATTCTCACAGCTT
3' ss Score
7.97
Exon sequences
Seq C1 exon
AGTCTCCTCCATCCACTGTCTCCAACACAGCCATGATTGCTGTCCTGGTTGTCCTTGGAGCTGTGACCATCATAGGAGCTGTGGTGGCTGTTGTGAGGAAGAGGAGGAGAAACACAG
Seq A exon
CTTTTCTTCTCACAG
Seq C2 exon
GTGGAAAAGGAGGGGACTATGCTCCAGCTCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000029001-2-4,2-3-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.165 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF066797=DUF1180=FE(63.3=100),PF066236=MHC_I_C=PU(3.7=2.6)
A:
NA
C2:
PF066797=DUF1180=PD(10.0=54.5),PF066236=MHC_I_C=FE(37.0=100)
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:
ACAGCCATGATTGCTGTCCTG
R:
CTGGAGCATAGTCCCCTCCTT
Band lengths:
118-133
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]