RnoINT0122908 @ rn6
Intron Retention
Gene
ENSRNOG00000000454 | RT1-DOb
Description
RT1 class II, locus DOb [Source:RGD Symbol;Acc:1595814]
Coordinates
chr20:4022319-4024504:+
Coord C1 exon
chr20:4022319-4022588
Coord A exon
chr20:4022589-4024222
Coord C2 exon
chr20:4024223-4024504
Length
1634 bp
Sequences
Splice sites
5' ss Seq
ATGGTGGGT
5' ss Score
6.18
3' ss Seq
TCTGTTTCTTCTCTTGCTAGTGC
3' ss Score
9.21
Exon sequences
Seq C1 exon
AGGATTTTGTGATTCAGGCGAAGGCAGAGTGTTACTTCACCAACGGTACAGAAAAGGTCCGCTTCCTGGTCAGGTTCATCTTCAACCTGGAGGAGTACTTACATTTCGACAGTGACCTGGGGTTTTTCGTGGCACTGACGGAGCTGGGGGAGGTGGACGCTGATCAGTGGAACAAACGCCTGGATCTCCTGGAAACAAGTAGAGCTGCTGTGAACATGGTCTGCAGGCAAGAGTACAAGCTGGGGGCCCCCTTCACCGTGGAGAGAAATG
Seq A exon
GTGGGTGAAGGGGAGGTCTAGGGGTTCTCTGGAAGAACCTCATACTAGGCATTTAAGAGGTCTTAACTATCCTCTGTCTGTCTGTCTGTCTATTACTTATTTGTGTGTGTTCCGTGCATGCCACAGTGCACACATGGAGGTCAGAGGACAATTCGAGGAGTTGGTTCTCTCCTTCCATCACGAGGATCCTAGAGATTGAACTCAGGTCATCAGGCTTGGGGGCGTCTGTGACTATGCTCTGTCCTCAGCTGTGAATTATTGGCTTAGATTTTTAAAACCTGCTTTAATAAGGGTTTGAAAACACTTCAACCTCCCTTCTAGCCCACCACCCATCACAGGTAGTGGGAAGGAAGGTTAATAGGAAACAGGGGTTGTGGACCTGCTTAGAAGTAGTTCTTTGGGGGCTGGAGAGATGTCTCAGTGGTTAAGAGCACCGACTGCTCTTCCAGAGGTCCTGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCTGTAATGGGATCCGATGCCCTCTTCTGGTGTGTCTGAAGACAGGTACAATGTACTCATATACAAAATAAATAAATAAATCTTTAAAAAGAAGTAGTTCTTTGGGAGCTCTTCCAGCCTTCACAGTCCGGTTCTCTAGCAAACACCAACACGAATCAGCCGCAGCAGTCTAGTCCACTTGGCAATCACCACTCATGGATCGGCAGTGGCGGTTTGATCCAGAAGAAACCGCAAGGCTCTGCCAATTGGCCGGAGTGTGTGGAAATAGGAAGAAGCTGCCGGGGTATCACGAGAAGTTCTTTGGCAAGTCACTCTCTATGGAGTCATGGCAGGCAAAGATACAAGCAAACCAATACAAGAGTGTCCTCAGGGAGGCAGAGCAAGGCGAACTAATGCCACAACCACCCCCCACTGTCTGTGGGCCATATTTATATTCTTCCCCTGCAAAATCACGCTTTCTCTCTCTCGTCTGCTTCTGCAAAACAACCTCTCACCTGTGTCAGCTTCAGCACAACATCCTCTGACACAGCCGAGATTCCAAAGAAACCAGAAATTTCCACCTCAGTGAATGGTGGTCTCCTTCTAGAAACCTCAGAGTTCTTGGGGTCTTTGAGAAATAGTGTCCATTGAATACAGTGGGTGACTGGGTGGAGGGGGTGACCTGGCAGAGTGTGAATCCTCCTTGTGTGTTGGGAGCAGTGCAGTAAAACAAAGATGGTGCCGACATCCAGTCCCGTCTGGTGGTAAACAACTTATCTCGCATGTGCAGGCTTGTCCCTTTGCCAGGGCGGCCGCAGGCTAATGGGGTGATTCGTGCTCTGCCAATCCCTGAAGGACAAGTAGCACGACCACAGCCTGTTGTGTATATAAGGCGAGCGCCTTTGCTGCTCGAGGTACCCGTATCAGCAAAGAGGTGGTCCTGCAATAAAGGGCTGTTGAGAAGAATCGGACTGTGTTGCGTCTTCCTTGCTGGCCGAGGTGGGCGCGACACTTGTGGGCCTCTTCTGCTTCTCAGTCTAGGGGCTTGGGGACCCCACCTTCCAGCTTCTATTTGGCTGGTTTGAGATACAGATCAGGGCGGTCAGGGTCTCTAGGGACGCTCCTGTCCCTGCTGTGCTTTCTGTTTCTTCTCTTGCTAG
Seq C2 exon
TGCCTCCGGAGGTGACGGTGTACCCAGAGAGGACCCCATTGCTGCAGCAGCACAACCTGTTGCTCTGCTCTGTGACAGACTTCTACCCTGGGGACATAAGTGTCAGGTGGTTCCGGAATGGGCAGGAGGAGAGGTCCGGGGTCATGTCCACTGGCCTTGTTAGGAATGGAGACTGGACCTTCCAGACGACGGTAATGCTGGAAATGATCCCAGAGCTTGGAGACGTCTACAGTTGCCTTGTGGAGCACCCCGGCCTCCTGAGACCTGTTTCTGTGGCATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000454:ENSRNOT00000000526:2
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=0.000
Domain overlap (PFAM):
C1:
PF0096914=MHC_II_beta=WD(100=82.4)
A:
NA
C2:
PF0765410=C1-set=WD(100=87.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCTGCTGTGAACATGGTCTG
R:
GCCACAGAAACAGGTCTCAGG
Band lengths:
345-1979
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]