RnoINT0122889 @ rn6
Intron Retention
Gene
ENSRNOG00000050210 | RT1-CE10
Description
RT1 class I, locus CE10 [Source:RGD Symbol;Acc:1359292]
Coordinates
chr20:157129-157665:-
Coord C1 exon
chr20:157602-157665
Coord A exon
chr20:157399-157601
Coord C2 exon
chr20:157129-157398
Length
203 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
TCACCGCGCGCCGCCCCCAGGCT
3' ss Score
8.13
Exon sequences
Seq C1 exon
ATGGCACGGCCCACGCTGCTCCTGCTGCTGGCCGCCGCCCTGGCCCCGACCAAGACCCGCGCGG
Seq A exon
GTGAGTGCGGGGTCGGGAGGGAAACGGCCTCTGGGGTAGGGACGGCTGANNNGNNNNNNNCNNCTGNNCCCCGCGTCTCACACCAGACCGCCCCGTCCCTTCCCCACCCGTGTCCCGAGCCCGGCGCCCTGCTCCCCGCCCGGCTGGCGCACCCGCCCGGGGTCCCGGGAGGAGGTCGGGGTCTCACCGCGCGCCGCCCCCAG
Seq C2 exon
GCTCACACTGGATGCGGTATTTCCACACCGCCGTGTCCCGGCCGGGCCTCGGGGAGCCCCGGTACATCTCTGTCGGCTACGTGGACGACACGCAGTTCGTGCGCTTCGACAGCGACGCGGAGAATCCAAGATACGAGCCGCGGGCGCGGTGGATGGAACGGGAGGGGCCGGAGTATTGGGAGCGGAACACACGGATCGTCAAGGGAAAGGAGCAGATTTTCCGAGACAACCTGAGGACCCTGCTTGGCTACTACAACCAGAGCGAGGGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000050210:ENSRNOT00000048858:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.033
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
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:
CTGGCCCCGACCAAGACC
R:
GCCCTCGCTCTGGTTGTAGTA
Band lengths:
294-497
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]