RnoINT0122932 @ rn6
Intron Retention
Gene
ENSRNOG00000000763 | RT1-M3-1
Description
RT1 class Ib, locus M3, gene 1 [Source:RGD Symbol;Acc:3494]
Coordinates
chr20:1816522-1818037:-
Coord C1 exon
chr20:1817762-1818037
Coord A exon
chr20:1816798-1817761
Coord C2 exon
chr20:1816522-1816797
Length
964 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
CCCAACACTTCCCCACCCAGATC
3' ss Score
6.84
Exon sequences
Seq C1 exon
GTTCTCACATCCTGCAGTGGATGGTTGCCTGCGAGGTGGGGCCAGACATGAGACTTCTTGGAGCACACTATCAGGCTGCATATGACGGCTCGGATTACATCACCCTGAATGAGGACCTGAGCTCCTGGACTGCAGCAGACATGGTGGCTCAGATCACGAAGAGCGAGTTAGAGTCAGAAGGTAGAGCAGAATACTTCAGAGCCTATGTGGATGGAGAGTGCCTGGAGCTGCTCCATAGATTCCTGCAGAATGGAAAAGAGATTCTTCAGAGAGCAG
Seq A exon
GTATGGGGAACAACTAAGAACCACTTTTAGAAGCCAAGATATCCCCTCTACCGTACAAGTGAGGCTTGTTGTCTGGGGAGGGATCAGCTAGAATACTGCATAAGGAGGAGAATGAGTGCTAGTGGCTTTCCTGATCCAACATGAGAGAGTGACTGTCCTCAGGGCTGACCCTGCTTGCAGAATAGTTGAATCTGTCCCGGATGGAAGGAGAAAACACCCTGAAATAAACAAACGCACACACTTCCATCCAGTCTGCAACTCATTGTGAACCATGGCCTCCCTCAGGCCTGGTTCTCTGCTCACTCACCCCCAATGTCTTTGGAGGTCACCCTCCACTGATGCTGAGTCTCTCAGCTCAACCCAATTAGGACTAGAGATGGGAAATCTGAAGACTTCTACTTGATGCTGTCTTAGGGTTTCTATTGCTATAAAGAAACACCATGACCAAAAGCAAGTTGGGGAAAGACAGGGTTTATTTGGCTTACCCTTCCAGCACTGTTCATCGTTGAAGGCAATCAGGACAGAAACTCAAACTGTTGATCTACAGGGCATACAGGAGTGCTGCTTCTTGGCTTGCACCCTATGGCCTGCTCAGCTTGCATTTTTATAGGACCCAGGACCTCCCGTCCAGCCATGGCACCATCTACAATGAGTTGGGCCCTGAAGCATCAATCACTAATTAGGAAAATGACCTATAGACTTGCCTACAATCTGATCTTTTATTAATGGAGGTACCCTCCTCTCATATAACTTTAGCTTGTGTCAAGTTGACATAAAAACTATTTAGTACATTAACCCTGATTTTAGAACATTCCAAGGAATGGATTATGCTAGGTACCAGAATCGGTTCCTGTATGGTGCTTACATTCCTTTTGTAGCCTAATTCTGACCATCCCAAGGATGCTCACATGAGCTCCAATGACTCCCTTAAAATGCTTTTTTCTCCCAACACTTCCCCACCCAG
Seq C2 exon
ATCCCCCAAAGGCACATGTGACCCTTCACCCAAGACCTGAAGGTGATGTCACCCTGAGGTGTTGGGCCCTGGGCTTCTACCCTGCTGACATCACCCTAACCTGGCAGTTGAATGGGGAGGACCTGACCCAGGACATGGAGCTTGTGGAGACCAAGCCTTCAGGGGATGGAACCTTCCAGAAGTGGGCATCTGTGGTGGTGCCTTCTGGAGAGGAGCAGAAATACACATGCCATGTGGAGCATGAGGGGCTGCCTGAGCCTCTTGTCCTGAAATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000763:ENSRNOT00000000990:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.011 A=NA C2=0.194
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(49.2=94.6)
A:
NA
C2:
PF0765410=C1-set=WD(100=93.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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:
GACATGGTGGCTCAGATCACG
R:
CAGAAGGCACCACCACAGATG
Band lengths:
346-1310
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]