RnoINT0140939 @ rn6
Intron Retention
Gene
ENSRNOG00000023548 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:RGD Symbol;Acc:1566079]
Coordinates
chr9:100423471-100424533:+
Coord C1 exon
chr9:100423471-100423583
Coord A exon
chr9:100423584-100424251
Coord C2 exon
chr9:100424252-100424533
Length
668 bp
Sequences
Splice sites
5' ss Seq
CCCGTAAGC
5' ss Score
4.37
3' ss Seq
TCTGTCCATTCCTCATCCAGGGC
3' ss Score
10.12
Exon sequences
Seq C1 exon
GGACCTGCTGCCAGGGAGAAGATACAGTGTGCGGCTAACCACCCTCAGTGGGCCTGGAGGAGCTGAATATCCTACAGAGAGCCTGGCCTCAGCTCCGCTGAACGTGTGGACCC
Seq A exon
GTAAGCAGACAGGCAATTCCTGCCTTCAGTAGTCACATACGTACCCTCGAGACCCAGGGCTTCCCTCCTGGCATCCTATCCTGCCCAAAGTGTCCTTACACTGTAAACTCAGACCCTGACCTCCTTGAGATCTCTTCACTTGGATGGGCAGGGGGAGAAGCCTTCTGCCAGAGACATTGTTTAAGACTGCACCAGCACCTGAATACAGCAAGATGTTCCTCAGTATGCCTTTAAGGAGCAAACTGGGATGATGTCACTAGGGTTTTGGGTCATGTGACCAGCCCACTCCGGCTACATTTCTTGGTATTACTGGTCCATGTGCCCTTTCCGTTGTATGAATTGTGAAGAGTGTGAGAGCAGTGGGAATTTACAAAGCAAGGATGACTACTAGGTACAACTCTGTGCCTCCCAGACTCAGGACTGCCCATCTGTGGCCCTCAGACACTTGGGGAGCATGTTTGAGGCATGACCTAACTTTTGCATACAGGATCCCTGTGCCATACACCCCCCCCCCCAGATGACAGGATGACAGCATTAACTAGGATGACAGTAGGCAGTAACGAAGGCTGTCTTCAGATGCAGCTCCAGATCCCTCACAGTCCTTAGATCATGTTTCACTACATGCCCTTTGACCTCTCACCACTTCCTTCTGTCCATTCCTCATCCAG
Seq C2 exon
GGCCTTTGCCTCCAGCAAACCTGACTGCCTCTCGAGTCACAGCGACCTCTGCCCATATGGTCTGGGACCCGCCCACTCCAGGCATCTCACTGGAGGCTTACGTCATCAATGTGACCACCAGTCAGAATACCAAGAGCCGCTACATCCCCAATGGGAAGCTGGTGTCCTATACGGTGCGTGATCTGATGCCAGGTCGGCGGTACCAGCTCTCGGTCACAGCGGTGCAGAGCACAGAGCAGGGCCAGCTGCACAGTGAGCCTGCGCACCTCTACATCATCACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023548:ENSRNOT00000022290:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.231 A=NA C2=0.421
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(27.4=59.0)
A:
NA
C2:
PF0004116=fn3=WD(100=86.3)
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:
GGGCCTGGAGGAGCTGAATAT
R:
GATGATGTAGAGGTGCGCAGG
Band lengths:
342-1010
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]