RnoINT0140932 @ rn6
Intron Retention
Gene
ENSRNOG00000023548 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:RGD Symbol;Acc:1566079]
Coordinates
chr9:100420335-100421179:+
Coord C1 exon
chr9:100420335-100420448
Coord A exon
chr9:100420449-100421065
Coord C2 exon
chr9:100421066-100421179
Length
617 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGA
5' ss Score
9.14
3' ss Seq
TGCCACCCCTGTCTGTGCAGAGA
3' ss Score
8.14
Exon sequences
Seq C1 exon
AAGTAGATGAGTGCCAGTCTCAGCCATGCCTGCATAAAGGCTCCTGCCAGGACCTCATTGCTGGTTACCAGTGCCTCTGCAGCCCGGGGTACGAAGGAGTCCACTGTGAGCTAG
Seq A exon
GTAAGAGGTCTGCTGAGGCTTTTGGGGTTCCTCAGCTATGGCTACCTTGTCACACCATCCTTCCCCGGGACAGAACTCTTGTCTAAATAACTATCCCATTCACTGCTTGCTCTCTGGCCATTCTGCTGGCCAGGATAGAGTTTAATGCTCTCTGTCCCCTCTTGCCCTGGAGACTGAGAGCTCATCAGACTCAGGCCTGGGGAGGGGTTGGTGGTGGTGGAGTTACCCGGTGCTCCCAGTTACTGGAGGGAGCAGAGGTCTGACCAATATAAGGCAGGGTGAGACTTTCATCCCTTGTGCCCGTGTGGGGCTTGAAGCTAGGAAACGGAGACCCTGGCTTCCTGAAGGGCAAAGCCTAGGAGCTGCTTCCACAGGTGACGGTAGGGAGCACAGAGCACACACAGAAGCAGCGATGAGGGTGTTAGGTGCTGGAAATGGGCAGCGAACCAACCAAGGAGGAGCAAGTGGATGTGACAGGAGAAAGGCTGTGGTTCAGAGTAGAGCATCCAGGCACTAAGGCCTCAGGGCCTTGCTGATCCTTAGGGAGCAAATAGAATGAATCCTGGGGTCCATGCAGGTAGTTCCAATGTGAGTCAGTGCCACCCCTGTCTGTGCAG
Seq C2 exon
AGACAGACGAGTGCCAAGCACAGCCCTGCAGAAATGGAGGCTCCTGCAGGGACCTCCCCGGGGCTTTCATCTGCCAGTGCCCTGAAGGTTTTGTTGGAACCCACTGTGAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023548:ENSRNOT00000022290:17
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:
PF0000822=EGF=WD(100=79.5)
A:
NA
C2:
PF0000822=EGF=WD(100=79.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGATGAGTGCCAGTCTCAGCC
R:
TGTTTCACAGTGGGTTCCAACA
Band lengths:
223-840
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]