RnoINT0081587 @ rn6
Intron Retention
Gene
ENSRNOG00000048951 | LOC100364500
Description
RT1 class I, locus CE11-like [Source:RGD Symbol;Acc:2320860]
Coordinates
chr20:2706390-2707120:-
Coord C1 exon
chr20:2706838-2707120
Coord A exon
chr20:2706669-2706837
Coord C2 exon
chr20:2706390-2706668
Length
169 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGT
5' ss Score
10.49
3' ss Seq
CTGACCGCGGGGTCCCGCAGGAT
3' ss Score
6.08
Exon sequences
Seq C1 exon
GCGCCGCCCCCAGGCTCACATTCGATGCGGTGTTTCAAAACCGCCGTGTCCCGGCCGGGCCTCGGGGAGCCCCGGTTCATAGCTGTCGCCTACGTGGACGACACGGAGTTCGTGCGCTACGACGGCGACGCGGAGAATCCGAGGACCGAGCCGCGGGCGCGGTGGATGGAGCGGGAGGGGCCGGAGTACTGGGAGGAGGAGACACGGAAAATCAAGGGACAGGAGCAGTGGTTCCGAATGAGCCTGAGGATCTTGCGCGGCTACTACAACCAGAGCGAGGGCG
Seq A exon
GTGAGTGACCCTGGTTCGGAGGTCACAATCCTTCCGGGTCCCCACACGGCCGGAGACTTCCGGTTCCCAAGTCCGAGGTTTGGGAGCAGAACAGACCCCGGCCGGTTTCCCTTTCGGTTTGGAGGAATCCGAGGGCAGGTGGGGCCGGGCTGACCGCGGGGTCCCGCAG
Seq C2 exon
GATCGCACACCTTCCAGAAGATGTCCGGCTGTGACGTGGGGTCAGACGGGAGCCTCCTCCGCGGGTATAATCAGTACGCCTACGACGGCCACGATTACATCGCCCTGAACAAAGACCTGAAGACCTGGACAGCGGCGGACTTTGCAGCACTGATCACCAAAACCAAGTGGGATCAGGCTGGTACTGCAGAGAGAAAGAGGGCCTACCTGGAGGGCACGTGCNNTGTGGAGTGGCTCCGCAGATACCTGGAGCTCGGGAAGGAGACGCTGCTGCGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000048951:ENSRNOT00000048535:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.341 A=NA C2=0.032
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(50.0=94.7)
A:
NA
C2:
PF0012913=MHC_I=PD(49.4=94.7)
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:
GGTTCATAGCTGTCGCCTACG
R:
GTCACAGCCGGACATCTTCTG
Band lengths:
245-414
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]