RnoALTA0032576-2/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000000763 | RT1-M3-1
Description
RT1 class Ib, locus M3, gene 1 [Source:RGD Symbol;Acc:3494]
Coordinates
chr20:1816522-1818037:-
Coord C1 exon
chr20:1817762-1818037
Coord A exon
chr20:1816691-1816797
Coord C2 exon
chr20:1816522-1816690
Length
107 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
CCCAACACTTCCCCACCCAGATC
3' ss Score
6.84
Exon sequences
Seq C1 exon
GTTCTCACATCCTGCAGTGGATGGTTGCCTGCGAGGTGGGGCCAGACATGAGACTTCTTGGAGCACACTATCAGGCTGCATATGACGGCTCGGATTACATCACCCTGAATGAGGACCTGAGCTCCTGGACTGCAGCAGACATGGTGGCTCAGATCACGAAGAGCGAGTTAGAGTCAGAAGGTAGAGCAGAATACTTCAGAGCCTATGTGGATGGAGAGTGCCTGGAGCTGCTCCATAGATTCCTGCAGAATGGAAAAGAGATTCTTCAGAGAGCAG
Seq A exon
ATCCCCCAAAGGCACATGTGACCCTTCACCCAAGACCTGAAGGTGATGTCACCCTGAGGTGTTGGGCCCTGGGCTTCTACCCTGCTGACATCACCCTAACCTGGCAG
Seq C2 exon
TTGAATGGGGAGGACCTGACCCAGGACATGGAGCTTGTGGAGACCAAGCCTTCAGGGGATGGAACCTTCCAGAAGTGGGCATCTGTGGTGGTGCCTTCTGGAGAGGAGCAGAAATACACATGCCATGTGGAGCATGAGGGGCTGCCTGAGCCTCTTGTCCTGAAATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000763-4-5,4-4-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.011 A=NA C2=0.194
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(49.2=94.6)
A:
NA
C2:
PF0765410=C1-set=WD(100=93.5)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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:
GACGGCTCGGATTACATCACC
R:
GTTCCATCCCCTGAAGGCTTG
Band lengths:
258-365
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]