RnoINT0122937 @ rn6
Intron Retention
Gene
ENSRNOG00000060412 | RT1-M4
Description
RT1 class Ib, locus M4 [Source:RGD Symbol;Acc:1562593]
Coordinates
chr20:2044030-2044803:+
Coord C1 exon
chr20:2044030-2044296
Coord A exon
chr20:2044297-2044524
Coord C2 exon
chr20:2044525-2044803
Length
228 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
GACCTCTTTGGCTTCAACAGAGT
3' ss Score
6.77
Exon sequences
Seq C1 exon
GCTCACACTCCCTGCGGTATTTCACCACCACCTTGTACGATCCTGGCTACCGCAAACCTCGGTTCACCGTCGTGGGCTACGTGGACAACACACAGATCGTGAACTTCGACAGCCACTTGGCGAGTCAGCGGGTGGAGCCGCGGGTGCCGTTTATAGCGCAGGATCCTGAGCATTTGGAGGAGCTGACACGCCTAGGCAGGGGGATCTTAATACTTGGCCGAATCGAACTGTGGACCCTGTTCGGTTACCATAGCCAGAGAGAGAATG
Seq A exon
GTAAGTGACCCCATACTCAGAAGGCTAGTCTACAGTCTCCGCGTATTCCTATGGAATATATACCCTGAGTTGGTGAAATCTGCAAGTTCCTGCCAGCCTGGAGATGCCTGCAAAAATTTACTGTGGTTTCATTTCAGTTTGAAATAGGCTTTGACCAATCACGCGCAGGCTATGTGCAATGAGCGGGACTAACCTAGGACACGGTGTTGACCTCTTTGGCTTCAACAG
Seq C2 exon
AGTCTCACACTGTCCAGTGGCTATTCGGCTGTGACATAGGGCCAGACCGTCGCCTCCTCCGTGGGTATAAGCACGTTGCTTATGAAGGCCAGGATTACATCTCTCTAACTGAGGACCTGCGCTCCTGGGTTGCGGTGGATACCGAGGAGGCTCAGATCACCAGGCGCAAGTGGGAGGCATCTGGTATTGCTACATCATGGAGGTCTTTCTTGGAGGGCAGGTGCGTGAAGTGGCTTCTCAAATACCTGGATAAAGGGAAGGAGATGCTGCAGCGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000060412:ENSRNOT00000030174:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.007 A=NA C2=0.021
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(49.7=98.9)
A:
NA
C2:
PF0012913=MHC_I=PD(49.7=94.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
CCTGAGCATTTGGAGGAGCTG
R:
GCAATACCAGATGCCTCCCAC
Band lengths:
293-521
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]