RnoINT0140936 @ rn6
Intron Retention
Gene
ENSRNOG00000023548 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:RGD Symbol;Acc:1566079]
Coordinates
chr9:100422133-100422857:+
Coord C1 exon
chr9:100422133-100422246
Coord A exon
chr9:100422247-100422578
Coord C2 exon
chr9:100422579-100422857
Length
332 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
AGAGCTCCTCCCACCAACAGCCC
3' ss Score
5.61
Exon sequences
Seq C1 exon
TGAGTGACCCCTGCTTCTCTAGCCCCTGTGGGGGCCGCGGCTACTGCTTGGCCAGCAACGGGTCCCACAGCTGTACCTGCAAAGTGGGCTACACAGGCAAGGACTGCACCAAAG
Seq A exon
GTGAGGGCCAGGAGCTCCGGGAAGGAGGATGGAGGAGCAAGGGGGCCAGAAGGTAGGCCAGGGGCCAAGTGGGAAAGATGGGCAGGCAGTTGCTGACCTAGGTCCCCTTCAGAGCAGGGAGGGGGCACTAACAGCCACATGTGTAGAAATGCAAACCTCCAAAGGGCCATGTGGCCCCAGTGAGAAGACTCCCTGCTAGGAATGATCTGGGTGACCAGGCCCCAGGGCCAATCTAGGTGACTTGACTGGGAGCTACTCTTCCCTGCTTAAAGGCTAACCCCTCCACCTCCTTTGTGTTTGGTGCAACCTTGAAGAGCTCCTCCCACCAACAG
Seq C2 exon
CCCTCAGGGTAGAAAGGGTGGAGGAGAGTGGGGTCTCCATCTCCTGGAGCCCACCCGAGGGCACCACGGCCAGACAGGTGCTGGACGGCTATGCAGTCACCTATGCCTCCTCGGATGGATCGTCCAGGCGCACGGACTTTGTGGACCGGAGCCGCTCCTCTCACCAGCTTCGGGCCCTGGCAGCCGGCCGTGCCTACAACATCTCTGTTTTCTCAGTCAAGAGAAACACTAACAACAAAAATGACATCAGCAGGCCTGCAGCCCTGCTCACCCGCACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023548:ENSRNOT00000022290:20
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=0.234
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=79.5),PF0004116=fn3=PU(2.4=5.1)
A:
NA
C2:
PF0004116=fn3=PD(96.4=85.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTTCTCTAGCCCCTGTGG
R:
GGCCTGCTGATGTCATTTTTGT
Band lengths:
358-690
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]