RnoINT0130982 @ rn6
Intron Retention
Gene
ENSRNOG00000001064 | Sbno1
Description
strawberry notch homolog 1 [Source:RGD Symbol;Acc:1310005]
Coordinates
chr12:37613018-37614763:+
Coord C1 exon
chr12:37613018-37613114
Coord A exon
chr12:37613115-37614602
Coord C2 exon
chr12:37614603-37614763
Length
1488 bp
Sequences
Splice sites
5' ss Seq
AATGTATGT
5' ss Score
5.87
3' ss Seq
ATTTTAAAATCTTTGTCTAGTAA
3' ss Score
4.39
Exon sequences
Seq C1 exon
AAGGTTCCTGTTGTGAGAGAAGAAGATGAACCAGAAGAAGAAGATGAGGAAGAAATGGGTCATGCAGAAACCTATGCAGAGTATATGCCAATAAAAT
Seq A exon
GTATGTCTTTGGATTTGACAAAATGACAGACTTAAGTTCCTCTTGAACTTAATTGTCTTAAACCGTGATAGTTAGTGCCTGACAAAGTCAAGTGCCTCAGGATTTGACAGATGTGAGCTATGAATAATTCTTTCCTCATCTCTACTCCCCCTCCCCCTTTCTTTTTCTAATGGACAAGGTCCTGTGAAGTCCAGACTTGCCTCAAATGGGCATTCCTCTTGCCTTGGCCCTACAGTTGCTGGGTGGGATTGCAATCATCCCACAATACCTTGTTCTGGTTTCAATGGAATTTACCTTTGGGAAATTTTACTCTGTGTTCCCTCTTCTAGACAAACTTAGAACCTTGTTTGAGGTTAAAGTCTTTAAAAGCCATGACAGTAAGTCCTTGGGTTTGTTTATTTTGTTGCTAGCTAGTTTCGCTTATGTAAGTATTGATCATAAAATTAAGGTGAATTATGGAGATACAAATATGCATTGTGAGTTTACACTAGTTTTCGCACCTTGTCCAAATCATAGGCACACTGAAACCTTCTTTTGATTCTTGAGAGTTTTTTTTTTTGTTTTGTTTTGTTTTTTTGGTTCTTTTTTTTTTTTTTTTTTTTTTTCGGAGCTGGGGACCGAACCCAGGGCCTTGCGCTTCCTAGGCAAGCGCTCTACCACTGAGCTAAATCCCCAACCCCGATTCTTGAGAGTTTTGATGTTTGTCCTTGAGACAAGTTCTTTTTGTGCTTGGAATTCTCAGTAAGGCTGACCTCCAACTCCTAGAGAGCTACTGTCTGAGTGCTTGGTGTGCTGGGCTTATCGGTGTGACCTGTCTTGCCTGGGGTCCATACCCTTTTGTGTTGGTTTACTGAGATAGTCTTTGTTTTAAGCTTGTGCTTGCTTTGTTCCCGAGTCAGTTCTATACTGGGATGTTTGCCATCAAGAGCCACTAGGCTTGACTTCGTTGGTTTTTATTAATGCTATTTTCCTGTCTTTTATGTAATGTGAATAACTTTTTGGTGGTCATTATATGAGGTGGAAAGTTAACTTTTAGTTTTTGCATAGAAATTTAAACCTTTTTGCTATATTAAGAGTAATAAGAGGGAAAATTGTTTATATATTTTTTTTAACCTTTTGATATCAGGTTTCCTTGTATTCCGTTTGTCCTTCAGCTCATGATCTCAACCACCTCATCTCTCATGGTAGATGGAGACTGGTGGTGTGCGGTACCATATCTAGCTACGTTTGGTTGTGTGGGGCCTGTCTGGGCCTCCTGAGGAAGTCTGCTTTTAAACTAAGTCTTTTCATTGTCCCATCTCTAAACTGTGTAGTTAGGTAACTTTTGTCAAATTTGAGAGGTACATTGCAATTAGTAACTTTTTATAGAAGCTCAAAGTGAGTAGTTAGTGTTTTCTCTGTCATAAGACAGATATCATACTATCTTGTAATACGACTGGAAATGTTATTAGAATGACTTAAATGAAACATTTTAAAATCTTTGTCTAG
Seq C2 exon
TAAAAATTGGCCTGCGTCACCCTGATGCGGTGGTGGAGACAAGCTCACTGTCCAGCGTCACTCCTCCTGATGTTTGGTACAAAACGTCCATCTCTGAGGAGACCATCGATAATGGCTGGCTCTCTGCATTGCAGCTTGAGGCAGTCACCTATGCGGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001064:ENSRNOT00000057902:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.727 A=NA C2=0.037
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF138721=AAA_34=PU(16.2=92.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGTTCCTGTTGTGAGAGAAGA
R:
CTGGGCCGCATAGGTGACTG
Band lengths:
257-1745
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]