RnoINT0122960 @ rn6
Intron Retention
Gene
ENSRNOG00000000777 | RT1-S3
Description
RT1 class Ib, locus S3 [Source:RGD Symbol;Acc:735037]
Coordinates
chr20:3178618-3179818:+
Coord C1 exon
chr20:3178618-3178665
Coord A exon
chr20:3178666-3179284
Coord C2 exon
chr20:3179285-3179818
Length
619 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGA
5' ss Score
9.11
3' ss Seq
CTCTTGTTCTATTGCTTCAGACA
3' ss Score
7.78
Exon sequences
Seq C1 exon
GCAGCAAGGCTTTCCAGATCTCTGACTGGCCTCAGAAGGCATGAAAAG
Seq A exon
GTATGAAAACCCATGGGGGCCTGGGATCGGACCTGAGGCAAAGGGAAGAACAGGGCCTTGTGGGATGATGTCACAGGTGAGGCAGGTACAAGATAGAAGGAGGCCTGTCATTGGATGAGAAAGAAGGATGGGTGGGAGAAAAGTTTGAAGGAAGAAGAGGATACTGGAACAGAGAGAGAGGAGGAGAGGAGGGAGAGGGAGAGAAGCCTTGGCAGGACAATATATCAGGTGACGTTAAGATTCTGCTCTGTGTACTTAGAGGTTGTTATTAATGTTCCTAAGGGATGGATGGTACCGGGCTTTGTATGTTTAAGTGGGCAATTATATCTTATCAATTGGATCTAAGATTATTGTGTGGTGTGTTCTTTTATGTGATGGTTTGAGTGTAGGAAAGTGTGCAGTGACAAGAGACGATGGGCCAGCACAGAGTTGGGATGTGTTTCCACCAAGATATCTAACAGATATCTTGGGGCATTGCAGTGCAGACCTAGCGGGGTAAAAGACAACTATACTTTTTTTACTTTTTATATTTTTACAACAACAGGGTCTCTCAGATTTAGACATTTGAATGACTGGGCATCTTTACAATGACTTCAGGACTCTTGTTCTATTGCTTCAG
Seq C2 exon
ACAGTTGCCTCGTGGGGCTGAGCGACAAGTTCTGACTAAACATCTGAGGGAGCTGCTTCCCCTGAGGACAATGTGAAGAACTGGCAATCCCAGACCTTCTTGCCTCCCTGGACACCTGACTTCACAACAGAAAATAATCTGACTCTGGGCTGGGTGTTTCCTATTGCTTTTATCTGCACTGAGTGGAAATGCGGTTTCCAACAGTGTAACGCAGTACCGTTGTGTGGTGGTAGTGACATTGCACACAGGTTTGTGAGCTGGGGGTGTGATGTGCTTTTGTTACTGTAGGCAGAACAAGCTAGAAGTCCACCATTCCTCTTATGGTCATTGTTTTAAAACAAAACAAATGCTGGAGAGATGGCTCAGTGTTAAGAGCACTGACTTCTCTTACAGAGGTCCTGGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATATGTAATGAGATCTGATGCTCTCTTCTGATGTGTCTGAACACAGCTATATATGATAAATAAATCTAAAAAATATTTTTTAAATGAATAGGGCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000777:ENSRNOT00000001036:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
3' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=NA
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping 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:
CCAGATCTCTGACTGGCCTCA
R:
TGGACTTCTAGCTTGTTCTGCC
Band lengths:
344-963
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]