RnoINT0122950 @ rn6
Intron Retention
Gene
ENSRNOG00000000795 | RT1-N3
Description
RT1 class Ib, locus N3 [Source:RGD Symbol;Acc:1598370]
Coordinates
chr20:3167079-3167938:+
Coord C1 exon
chr20:3167079-3167439
Coord A exon
chr20:3167440-3167668
Coord C2 exon
chr20:3167669-3167938
Length
229 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TCACAATGTGCTACCCCTAGGCT
3' ss Score
7.58
Exon sequences
Seq C1 exon
GAACACACTTTATCAGCAAGGGTGAGGGCAAGAGGCTAGCAGGATGTAGGCCGGAGAATTGTCAGACCTGTTGGTGGCTTCTGCCACCGGAAGAATTTAGAACATAAAATAGATGATGGATTTGGGACAATAGATTCTGCACCCAGAGCTTCTGTCACTTGGTTACTTTTAAAATTAAGATTGCCTGGTGTTAGTTGGGTTCTGAGATTATCCAATCCCTGTCGCTCTGGTTTACAAAGTTGTCCAAGATCAGCCCAGACCCATATGCTCTGGGTTCCTAAGGCTGCTGCGCGCTGGCTCAGTGCCCTTCTCCAGATCCTGCTCCTGAATGCCTGCTTCTCCTGGACTTGGACCCTTGTGG
Seq A exon
GTGAGTGAGATTGGGGTGGGGCTGGGGGAGGGGGGGGGAAGGCCTCTGCTAGGAAGGCCAGGAGTAGCACCACCCAGTCTCTCCAAGACCCAGAAAGATCCTCCAGCCCTCTTCTCAACCTGCCCCGATCCCATCCCGATCCCATCCCGGAGCCCTGCTCCCCTACTGGCCCGCGCACCCTCCCGGGGTCATCTGTGGAGGTCTGGGTCTCACAATGTGCTACCCCTAG
Seq C2 exon
GCTCACACTCCCTGCGGTATTTCTCCACTGTCATGTCCTGGCCCGGCCTCCGGGAGCCAAGGATAATAGTCAGCGGCTACATAGATAATATGGAGTTCCTGCGCTTGGACAGCGACGCCGAAACTCCAAGGGTGAAGCCCCTAGTACCATGGCTGGAGCAGGAGGGGCTGGAATACTTGGAGCAGCAGATTCATAGAATCAGGACTCAAGCACAACAGTCTGAAAGGAACCTGATGACGCTGGTTCGTTTTTACAATAAGAGCATGGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000795:ENSRNOT00000001035:1
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=0.000
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(0.1=0.0)
A:
NA
C2:
PF0012913=MHC_I=PU(52.6=98.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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:
AGATCCTGCTCCTGAATGCCT
R:
AAACGAACCAGCGTCATCAGG
Band lengths:
298-527
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]