RnoINT0122909 @ rn6
Intron Retention
Gene
ENSRNOG00000000454 | RT1-DOb
Description
RT1 class II, locus DOb [Source:RGD Symbol;Acc:1595814]
Coordinates
chr20:4024223-4025542:+
Coord C1 exon
chr20:4024223-4024504
Coord A exon
chr20:4024505-4025431
Coord C2 exon
chr20:4025432-4025542
Length
927 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGC
5' ss Score
5.97
3' ss Seq
TAAGTCTCGTTTTCTCACAGTGG
3' ss Score
6.46
Exon sequences
Seq C1 exon
TGCCTCCGGAGGTGACGGTGTACCCAGAGAGGACCCCATTGCTGCAGCAGCACAACCTGTTGCTCTGCTCTGTGACAGACTTCTACCCTGGGGACATAAGTGTCAGGTGGTTCCGGAATGGGCAGGAGGAGAGGTCCGGGGTCATGTCCACTGGCCTTGTTAGGAATGGAGACTGGACCTTCCAGACGACGGTAATGCTGGAAATGATCCCAGAGCTTGGAGACGTCTACAGTTGCCTTGTGGAGCACCCCGGCCTCCTGAGACCTGTTTCTGTGGCATGGG
Seq A exon
GTGAGCATCCTTTTGTTTTCTGTATTTCTCAGCCTTGGCCTATATGGGCTGCCACTTCTGTGTTCATTTCATGTTGATGACAAGACACATTCCCCTGATATAATAATCCTAGTACCAGGGCAGGAGAAAACAGGACAGACATCCATCCTCCGAATGCCTGGGGGACAGAGAAGGAGGGCTGTTAACCCACAGCTTGCCTCTAAGCCCGGGACCTAGTATTCTTTAACATTTTAATCTTTAGGGACATTGTCACGGGCTGTAAATCAGGGAGAGACCTGGAGAAGTGTCTTAGCTGGTGAACGGCTTGCCACATAAGTGTGAGGACCTGAGATTGGTCCCCAAAGTCGATATAAAAAACCCAGGTGCTCTGGTCCCTGCTTGTAGTTCTAGGGCCTGGGGGTGTGTGTGTGGAGACAGGGAGCCTATTAGCATGCTCTAGGTCAGCCAGGGACATTGAACTATATAGCAAGAATAGCGAAGATGGCACCAGAGGAATAACACTGGAAGTTGACCTCTTGTCTATTGCATGCACGTGAACGTGCGTGCATGTGCACACACACGACACACTCATACACATACATAACATAGACATTTACACCCTTACACACATACATTCATGCAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGAGAGAGAGAAGGGAGAGAGAGAGAAGGGAGAGAGAGAGAGAAGAGGGAGAGAGAGAGAAGGGAGAGAGAGAGGGAGAAGAAGGGGGAAGAGGAGGGGGAGGGGGAGAGGGAGAGGGAATATCAGTGACCAATAGAAAGCGACTCCATTTCTAGATTTAGTTCTTCCCTGAGCAGTACTGGGCTTTGGGGCTTTAAGAAGTTGCGGCCAGAACTGGAAGCATCACATTGACTTTAAGTCTCGTTTTCTCACAG
Seq C2 exon
TGGCTCAGTCTGAATATTCCTGGGAAAAGATACTGAGTGGAGCTGCAGCATTCCTGCTTGGGCTGACTGTCTTTCTGGTGGGAGCTGTCATCCACCTCAAGGCTCAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000454:ENSRNOT00000000526:3
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:
PF0765410=C1-set=WD(100=87.4)
A:
NA
C2:
NO
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:
GTACCCAGAGAGGACCCCATT
R:
TGACAGCTCCCACCAGAAAGA
Band lengths:
353-1280
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]