RnoINT0130974 @ rn6
Intron Retention
Gene
ENSRNOG00000001064 | Sbno1
Description
strawberry notch homolog 1 [Source:RGD Symbol;Acc:1310005]
Coordinates
chr12:37641425-37641748:+
Coord C1 exon
chr12:37641425-37641571
Coord A exon
chr12:37641572-37641653
Coord C2 exon
chr12:37641654-37641748
Length
82 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGT
5' ss Score
8.83
3' ss Seq
TGTTTCTATCTTAATGTAAGATC
3' ss Score
3.67
Exon sequences
Seq C1 exon
ACTATAATAATATAGGAAAATTCTTAAACAGAATTCTGGGCATGGAGGTGCATCAGCAGAATGCGTTGTTTCAGTATTTTGCAGACACACTCACTGCAGTTGTTCAGAATGCCAAGAAGAATGGGAGATACGACATGGGAATCCTAG
Seq A exon
GTGAGTGGGACCCTCACTATACTCTGCTCCCGGGCCTGAGTGTCTCTCCATTTACACGCTTCTGTTTCTATCTTAATGTAAG
Seq C2 exon
ATCTGGGTTCTGGAGATGAAAAGGTGAGGAAGAGTGATGTCAAGAAGTTTCTGACTCCAGGATACTCAACCTCTGGCCATGTAGAGTTATATACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001064:ENSRNOT00000057902:26
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:
PF138711=Helicase_C_4=FE(17.7=100)
A:
NA
C2:
PF138711=Helicase_C_4=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAATTCTGGGCATGGAGGTGC
R:
CCTGGAGTCAGAAACTTCTTGACA
Band lengths:
178-260
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]