RnoALTA0032579-3/3 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000000795 | RT1-N3
Description
RT1 class Ib, locus N3 [Source:RGD Symbol;Acc:1598370]
Coordinates
chr20:3167079-3167938:+
Coord C1 exon
chr20:3167079-3167439
Coord A exon
chr20:3167669-3167780
Coord C2 exon
chr20:3167781-3167938
Length
112 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TCACAATGTGCTACCCCTAGGCT
3' ss Score
7.58
Exon sequences
Seq C1 exon
GAACACACTTTATCAGCAAGGGTGAGGGCAAGAGGCTAGCAGGATGTAGGCCGGAGAATTGTCAGACCTGTTGGTGGCTTCTGCCACCGGAAGAATTTAGAACATAAAATAGATGATGGATTTGGGACAATAGATTCTGCACCCAGAGCTTCTGTCACTTGGTTACTTTTAAAATTAAGATTGCCTGGTGTTAGTTGGGTTCTGAGATTATCCAATCCCTGTCGCTCTGGTTTACAAAGTTGTCCAAGATCAGCCCAGACCCATATGCTCTGGGTTCCTAAGGCTGCTGCGCGCTGGCTCAGTGCCCTTCTCCAGATCCTGCTCCTGAATGCCTGCTTCTCCTGGACTTGGACCCTTGTGG
Seq A exon
GCTCACACTCCCTGCGGTATTTCTCCACTGTCATGTCCTGGCCCGGCCTCCGGGAGCCAAGGATAATAGTCAGCGGCTACATAGATAATATGGAGTTCCTGCGCTTGGACAG
Seq C2 exon
CGACGCCGAAACTCCAAGGGTGAAGCCCCTAGTACCATGGCTGGAGCAGGAGGGGCTGGAATACTTGGAGCAGCAGATTCATAGAATCAGGACTCAAGCACAACAGTCTGAAAGGAACCTGATGACGCTGGTTCGTTTTTACAATAAGAGCATGGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000795-1-2,1-1,1-0-3/3
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
Mouse
(mm9)
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:
ATCAGCCCAGACCCATATGCT
R:
AAACGAACCAGCGTCATCAGG
Band lengths:
251-363
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]