RnoINT0122922 @ rn6
Intron Retention
Gene
ENSRNOG00000030431 | RT1-Db2
Description
RT1 class II, locus Db2 [Source:RGD Symbol;Acc:1595922]
Coordinates
chr20:4116941-4118506:+
Coord C1 exon
chr20:4116941-4117207
Coord A exon
chr20:4117208-4118224
Coord C2 exon
chr20:4118225-4118506
Length
1017 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
CACCTCTTTTTCTACTCTAGCTA
3' ss Score
8.65
Exon sequences
Seq C1 exon
CACGTTTTCTGGAGCAGTTGAAGGCTGAGTGTCACTACGTCAAGGGGAGGGAGCATGTGTGGAGCGTGACCAGATTCATCTATAACCAGGAAGAGTTTGCCCGCTTTGACAGTGTCTTTGGGAAGTTCCTGGCAGTGACTGAGCTGGGGCGGCCCATAGCTGAGTACTTGAACACCCAGAAGGACATGCTGGACAATTACCGTGCCTCTGTGGACAGGTGCAGAAATAACTATGACCTGGTTGATATCTTCATGTCGAACTTAAAAG
Seq A exon
GTAAGCATTAGATGGGAAGTAGATGAGTTAAGAGGTGTGTGTGTGTGTGTGTGTGTGCGCATCTGTGTGTGTATGTGTGTGCGTATGCATCTGTGCGTGCATCTCTGTGTGTGTGCATCTGTGTGTGTGCATTTGTGTGTGTGTGCATTTGTGTGTGTGTGCATTTGTGTGTATATGTTGTGTGCATTTGTGTGTGTGCATTTGTGTGTATATGTTGTGTGCATTTGTGTGTATATGTGTGTGTATATGTGTGTGTGTGCATCTGTGTGTGTGTATGTGTGTGTATGCATCTGTGTGTGTATGTGTGTATGCATCCGTGTGTGTGTGCATCTGTGTGTGTGCATCTGTGTATGTGAGCATTTGTGTGTGTGCATGTGTGTTTGTGTGTGTGTGTGTGTGTGTGTACGCATATCTATGTATGTATCTAGGGGGTGGGGGGAGGAGAACGCTGTGTCAATGTATGTATCTGGGGCTGGGGGAAGCACTGTGTCACGTGTGTAGAAATCAGAGGACAGCTTACCAGAGTCATTCTCTCTATCCATCATGTGGTCCCGAGAACTGAATTCAGATCATCGGTCTTGGAAGCAAGCACTTTTATCTGCTGAGCCATCTCCCTAGCCCTTACTGTAATGACTTTTTAACTTTTGCTGGCCTTGGGACCCCTGAGAATCACCGCTCTCTGCTCCTGCTTCCTAGGGTAGATCCATTCCTGAGCTGTTCTGTGGTGTGTGTGCTCTGAAGTTCTGTATTCCCAATCTAGTGAACACGCACTGCTTTCAGGCATGTTTTCAAACTGAAAATATTTCAGCTCAATAATGGATTATTAGTATTTGCTAAATAAATAAATCCTTACAGGTTTTTTTTAAGATCCATTGAGCCCTGGTGTCAGGATTAACTTGGGGGACAGGTTTAGAAGCTCTGCAAGATCTTCAGCCGGGGTGGATGGAGGCAGTCAGGTAGGCACAGGAAGGACAGCTCCACCCTCATGATTTCTTCTCACCTCTTTTTCTACTCTAG
Seq C2 exon
CTAAACCCAAGGTGACCGTGTACCCTTCAAAGACGCAGCCCCTGGAATACCACAACCTCCTGGTCTGCTCTGTGAGTGACTTCTACCCTGGCACCATTGAAATCAGATGGTTCCGGAATGGTGAGGAGGAAAAGACTGGAGTCGTGTCCACCGACCTGATCTCTAATGGAGACTGGACCTACCAGACCCTGGTGATGCTGGAGACGGTTCCTCAGGGTGGAGAGGTTTACACCTGCCAGGTGGAGCATCCCAGCCTGACCAGCCCTGTCAGAGTGGAGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000030431:ENSRNOT00000042571:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.030
Domain overlap (PFAM):
C1:
PF0096914=MHC_II_beta=WD(100=82.2)
A:
NA
C2:
PF0765410=C1-set=WD(100=87.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGAGCAGTTGAAGGCTGAG
R:
ATGGTGCCAGGGTAGAAGTCA
Band lengths:
356-1373
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]