RnoINT0122931 @ rn6
Intron Retention
Gene
ENSRNOG00000000763 | RT1-M3-1
Description
RT1 class Ib, locus M3, gene 1 [Source:RGD Symbol;Acc:3494]
Coordinates
chr20:1817762-1818509:-
Coord C1 exon
chr20:1818240-1818509
Coord A exon
chr20:1818038-1818239
Coord C2 exon
chr20:1817762-1818037
Length
202 bp
Sequences
Splice sites
5' ss Seq
GCAGTGAGT
5' ss Score
7.39
3' ss Seq
GACAGCTTGGTTGTGGCTAGGTT
3' ss Score
4.55
Exon sequences
Seq C1 exon
GCACACATTCACTGCGTTATTTCCACACTGCCCTGTCACGGCCGGGCCGTGGGGAGCCTCAATATATTTCTGTCGGCTATGTGGATGACAAGCTGTTTCAGCGCTGTGATAGCGTTGAGGAGATTCCGAGGATGGAGGCCCGTGCACCTTGGATGGAGAAGGAAGGACCAGAGTATTGGGAGGAGCTGAAACTCAAAGTAAAAAGCATTGCACAAAGAGCCAGAGCAAGACTTCGGACCTTGATCCGCTACTACAACCAGAGTGAAGGCA
Seq A exon
GTGAGTGACCCCAGGTCTGGGTTGGACTCTTATATGTCCCTACTGCTAAGCTAGATTAGCCCTGTGTCTCAGGTTTAAAGTTTGGTTGGACTTCAGAACCCTCATAAACCTTTAGTTGGTTTCACTTTCAGTTTTAGCCTAAATCTTGCTAGTGGGCAGATTGCGATGGGGTGGCCCAGACTGACAGCTTGGTTGTGGCTAG
Seq C2 exon
GTTCTCACATCCTGCAGTGGATGGTTGCCTGCGAGGTGGGGCCAGACATGAGACTTCTTGGAGCACACTATCAGGCTGCATATGACGGCTCGGATTACATCACCCTGAATGAGGACCTGAGCTCCTGGACTGCAGCAGACATGGTGGCTCAGATCACGAAGAGCGAGTTAGAGTCAGAAGGTAGAGCAGAATACTTCAGAGCCTATGTGGATGGAGAGTGCCTGGAGCTGCTCCATAGATTCCTGCAGAATGGAAAAGAGATTCTTCAGAGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000763:ENSRNOT00000000990:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.022 A=NA C2=0.011
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(50.3=98.9)
A:
NA
C2:
PF0012913=MHC_I=PD(49.2=94.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGCACCTTGGATGGAGAAGG
R:
GCTCTTCGTGATCTGAGCCAC
Band lengths:
293-495
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]