RnoINT0140940 @ rn6
Intron Retention
Gene
ENSRNOG00000023548 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:RGD Symbol;Acc:1566079]
Coordinates
chr9:100424252-100425819:+
Coord C1 exon
chr9:100424252-100424533
Coord A exon
chr9:100424534-100425674
Coord C2 exon
chr9:100425675-100425819
Length
1141 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
CCTTTCTCCTTTTTTGGCAGCCC
3' ss Score
8.43
Exon sequences
Seq C1 exon
GGCCTTTGCCTCCAGCAAACCTGACTGCCTCTCGAGTCACAGCGACCTCTGCCCATATGGTCTGGGACCCGCCCACTCCAGGCATCTCACTGGAGGCTTACGTCATCAATGTGACCACCAGTCAGAATACCAAGAGCCGCTACATCCCCAATGGGAAGCTGGTGTCCTATACGGTGCGTGATCTGATGCCAGGTCGGCGGTACCAGCTCTCGGTCACAGCGGTGCAGAGCACAGAGCAGGGCCAGCTGCACAGTGAGCCTGCGCACCTCTACATCATCACCT
Seq A exon
GTGAGTTAGTTCCCTGACAGGACGGCCTGGGATGCTGTTCAAACCCACGGCTGCTGTTTGCTGCTGTTGGGGTGTGGGATCCTTGCCCAGAAGAGGCAGCATAGACAACTTGCATGGGCCATTCCTCGGAACAGAGATGTAGGCATAAGGGTGAGGAAGGACAGTTGACAGCATGAGCCTCATCTTACACTGTTTTACCAGTCCAATCCCAGCAGGCTTAGCAGCAAATACAGGACCTCACCGTGAAAGAGCTACCAAGCAGGCAGCAATGCCGAGGCCCAGGCCTGACCCAAAAGGGGCCACTGGGCATGAACACCAGAGGGCGGGGCAAGAGACTACAAGTAGCTGGGTAGGGCAGGAAGGGTAAGAATGAAAAGCTGGGGTGTAGACATTCAGGTGGCCACATTAACAACCTCACTCTATTCCCAAGGTGACAGGGCACTCAGCTGGAGCCCAAAAGTGTCCTGTGTGCCCCTTATTACCTTCTCAAACCTTACGTGAGGTGCTGTATGAGAGAGTTTCAGGAGTGCAGGGAGCAGAACTCAGCGAGAAAACAAGCAGAAGGTGCACAAGAAAACAAGACAGCGGGTTCTCAGAGTCAGGCCAGTGCTCTCTAAGACAGTGAGGCTCCACTCCCAGCCTTCTGGGCCCCTCCTCCATTCTCATCCCAGCCCCAGCCGAGGCTGCTTTGTGAACTTGACAGTGAAGGCAGTGCTTATATACTAATTCTCACACCCAACCCTCTCAGAGTCAGGATGAGGCAGACAGAGAAGGAAGGAAGTCACTTTGCTTGAGAGTCCGAAGGGACATGACACTCAAGGGTGGTAAGGGCCTGGCTATAGGAAAGCTGCACATCAGGAAAACAACGATTGATCCAGTCTAGCCTCCACTTAGCAAATCAGGACTCTGCTGGGGAGTGGGGGGAGCTGGCCTTCCAGACCAGTGCATCTGCTGCAGCATAAATGCACAGCCTCTTCTCAGAAAGGTACAGCTTGTGACAAAGACTTCTTAGGCGATGTGCTCCTCTCTCTGCCCAGCCTAAGTGGGGCTGGGTTTGAGCTGCCACTTCTGCAGTAGGGGCAGAGACAGGAACACTAGGCAGCCTAGTTGGTGGCAACTCCCCTTTCTCCTTTTTTGGCAG
Seq C2 exon
CCCCCAGGGATGGCACCGACAGGCGCTGGCACCAGGGAGGACACCACTCACGAATGCTCAGAAATAGGCCGGCCCCTTTGCGCCTGCCAGAACTGCGCCTCCTCAATGACCACGGTGCCCCTGAAACACCAACCCAGCCACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023548:ENSRNOT00000022290:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.421 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=86.3)
A:
NA
C2:
NO
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:
CAGCAAACCTGACTGCCTCTC
R:
GCCGGCCTATTTCTGAGCATT
Band lengths:
343-1484
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]