RnoINT0130969 @ rn6
Intron Retention
Gene
ENSRNOG00000001064 | Sbno1
Description
strawberry notch homolog 1 [Source:RGD Symbol;Acc:1310005]
Coordinates
chr12:37632837-37633896:+
Coord C1 exon
chr12:37632837-37632972
Coord A exon
chr12:37632973-37633783
Coord C2 exon
chr12:37633784-37633896
Length
811 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGT
5' ss Score
11.78
3' ss Seq
TGTACACATTTTTGTTACAGGAA
3' ss Score
9.04
Exon sequences
Seq C1 exon
AATATTGCTATTATCTCAGAAGCTGCCAGCTCAGGTATTTCATTACAAGCAGATCGGAGAGCTAAGAATCAAAGGAGAAGAGTTCATATGACTTTAGAGTTACCCTGGAGTGCTGATCGGGCCATTCAGCAGTTCG
Seq A exon
GTAAGTATCTGCACTGCATCCCACTGGGAGGACAGATAAGAGTTTCTGGGAGTCTGTATGAGATACCAGGAGCCTATAGAATTCTCAGATTCTGTATTGGAAGTGTGTTCTCTGTATATATTGTGGTATGCAATGGATGATGAGCTCCTTTTTGCCTGTTTTCAAATGGTATTGAGATCTTTGATGGATTGCAAAGGAGTCCTGTCCTTCTAGAACAGGGTTCCCCAGAAGTATCTTCATTGTAGATTTGTACACCATTTGGGTCTTTCACAGCAGCCCACTATTTCCCCAGTTATTTTAGCTCTTAATAGCTCCATGAGGGCAACATTACTCTTCCTTTTCATATGCATGATCCTAAGACCTAGTGATCTGTCTACCCATGACATCCAAAGGGGTTATGCAGGAACACTAGCTAGCCAAATGGTGGCAGCATTTGGACATTTATGGCAGGCTCTGATCCTTGAGTCGTGATGCCAAGGTTTAAGAGTTTAAATTGCTGTTATAGGGACCTGGAAAGAGTTGTGTTACCTTTAATCTTTTTTAGGGTGTTTTGTTGGTGCTAACTTGGCCAGGTTGGCAGGCTTGTCCTCTGCACACAGGATTGGTAGACAGAGAAGTACCAGGGGTGTAAGGCCTGACGTAAACTGCATAGTGTGTTTGAGGCCACCCTGGACTACATGAGACCTTGTTACTACAAGTGACCTTGTCACTTTAATACCCTTTAAGTATTAAAGCTACAGTTAGGGTCTCAAAATAGCCTAATTTCTGTCCAGTGAGCATGATCATTGAACTGTACACATTTTTGTTACAG
Seq C2 exon
GAAGAACACACAGGTCAAACCAAGTGACTGCTCCAGAGTATGTTTTTCTGATTTCGGAGCTGGCTGGAGAACAGAGGTTTGCGTCTATTGTTGCTAAGAGACTTGAGAGTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001064:ENSRNOT00000057902:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.217 A=NA C2=0.079
Domain overlap (PFAM):
C1:
PF138711=Helicase_C_4=FE(16.2=100)
A:
NA
C2:
PF138711=Helicase_C_4=FE(13.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATATTGCTATTATCTCAGAAGCTGC
R:
ACTCTCAAGTCTCTTAGCAACAA
Band lengths:
246-1057
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]