RnoINT0122887 @ rn6
Intron Retention
Gene
ENSRNOG00000050183 | RT1-CE1
Description
RT1 class I, locus1 [Source:RGD Symbol;Acc:1595869]
Coordinates
chr20:4943018-4943564:-
Coord C1 exon
chr20:4943492-4943564
Coord A exon
chr20:4943288-4943491
Coord C2 exon
chr20:4943018-4943287
Length
204 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
CATCCGCGCGCCGCCCCCAGGCT
3' ss Score
8.3
Exon sequences
Seq C1 exon
ATGGGGGTGACTGCGCCGCCCTTGCTGCTCCTGCTGCTGGCGGCCGCCTTGGCCCGGACCCAGACCCGCGCTG
Seq A exon
GTGAGTGCGGGGTCCGGAGGGAAATGGCCTCTGCGGGGAGGGGCGGGGGCGGCACCGGGGAAGCCAAGTCCCTGCTTCGCACAACAGACCCTCCGCCGCTTCTCCACCCCAGTCCGGAGCCCCACGCCCTGCTCCCCGCCCGGCCCCCACACCCGCCCGGGGTCCCGGGAGGAGGTAAGGATCTCATCCGCGCGCCGCCCCCAG
Seq C2 exon
GCTCACACTCGCTGCGGTATTTCAAAACCGCCGTGTCCCGGCCGGGCCTCGGGGAGCCCCGGTTCATGGAAGTCGGCTATGTGGACGACACGGAGTTCGTGCGCTTCGACAGTGACGCGGAGAATCCGAGATACGAGCCGCGGGTGCGGTGGATGGAGCGGCAGAGGCCGGAGTATTGGGAGCGGGAGACGCAGGGAGCCAAGGAAAAGGAGCAGACTTTCCGAGTGAACCTGAGGACCCTGCTTGGCTACTACAACCAGAGCGAGGGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000050183:ENSRNOT00000049310:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.110
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(0.1=0.0)
A:
NA
C2:
PF0012913=MHC_I=PU(50.3=98.9)
Main Inclusion 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:
CCCTTGCTGCTCCTGCTG
R:
GGTCCTCAGGTTCACTCGGAA
Band lengths:
294-498
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]