RnoINT0140927 @ rn6
Intron Retention
Gene
ENSRNOG00000023548 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:RGD Symbol;Acc:1566079]
Coordinates
chr9:100412791-100414282:+
Coord C1 exon
chr9:100412791-100412907
Coord A exon
chr9:100412908-100414165
Coord C2 exon
chr9:100414166-100414282
Length
1258 bp
Sequences
Splice sites
5' ss Seq
AAGTGACTA
5' ss Score
-8.63
3' ss Seq
CTGTCTGTCTTTCCATACAGCCC
3' ss Score
11.68
Exon sequences
Seq C1 exon
CTCTGCCCTCGCCCTGCGACTCAGACCCATGCTTTAATGGAGGTTCCTGTGACGCCCACGAGGACTCCTACACGTGCGAGTGCCCTCGTGGATTCCATGGCAGGCACTGCGAGAAAG
Seq A exon
TGACTAGAGAGGGAGGGAAGTGGGGCACAGGATAGGGCACGGTAGATCTGAAGAGAAGCTGGGGGCGGAGCGGAGCGGGGCGGAGGCGGGGCGTGTGCCTCCGGTCTCTGCTGTCAGCACCACGGAGAGCTCCCAGCCTGCCGCGTTGCTAGCCTTTCCTTTCAGCAGATAATCATTTTGTTCTGGGACCTCCCTCAGCCTCTTTGCTCCACACATCTAGGACAGCTCGAGCCTTACCATTTTTGATAGTTATTTTCGTCACTTGTCCTGGTCTGTAAACCTCGATGGGCTTCACTTTCCCCTCATTATTTTTCCAGTAGATTTTAGAATCATTATATTGAACTTAAAATTTTTTCATTCTGATTTTGTTAAATTTAGTTTAACATAGAGAATGCAAACATTTTACAACATCTAAACACTTAGAATTTAAGTATTCTTCCAAAACATATTGCAGGGGTTGGCCTCTCCACCAGTGCCACCCAGGACTGTCCCTTTCCTGCAGCAGGACATAATAAAACACACCTCAAACCAGGCATCTTAGGAATGTCCTCTACTGAAGGCCTTTGTAACCTTGCTCAGGACTCTAGGCATCTCACAGCTCTGGCTGGTCAGGAGGACCAAGACCACAATGGATTTATTTATGAGGAGCCTCCCCATACCATCTCTTCAGCTAGCCCCAGAGCAGGTTTCTGACAGGGGTGCCTGAGACCCTCACAGTTTCCTCTGTCCTTGAAGTGACAGAGAGAGTTGCTAAAGAGAAGGCCTTCTGCATGGCTATCCCTGAAACCCCATGTAGGGCCCTTCTGGAATCTGCTCTGAGGGACCCTGAGGGAGACCTCTGTGTGCATTTGCTGAGGTGGCATAGGACTGGATGAGGCAGAGACACTGGACCCTGTAAGCCTGGCCTGGAGATAGGTGTGGTCTGTGGGTATGATGTCCCCTAGAACTGTGAACTCTGTGGCTGGAGGTCCAGAGCAGATTCTGGAAGGGACCTCTGTGTGTGTGCTGTGCTGTAGGGCTCAGTTTTCCAGCAGGGAGAGCACTGGCAGGCTTGGGCCGATAGCCTGAGCTCCATGCACCCTTTTTTTAAGCCTGACTGATTTAGCTTCTGCTGTGTTGAGCCTTGGAGTCCAGCTGAGCAGGTCTGTCTTTGGGTCCATTCAGTACCAAAGGACTGAAAAGGCAGCATGGTAACATGGATTCTACACCACTCAGAGGCTGGCTCATGTCCATCGTATCTGTCTGTCTTTCCATACAG
Seq C2 exon
CCCGGCCACACCTGTGCAGCTCAGGGCCCTGCCGGAATGGGGGCACATGCAAGGAGACTGGTGACGAGTACCGCTGCACCTGCCCTTACCGGTTCACTGGGAGACACTGTGAGATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023548:ENSRNOT00000022290:12
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=77.5)
A:
NA
C2:
PF0000822=EGF=WD(100=77.5)
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:
CCCTGCGACTCAGACCCAT
R:
AATCTCACAGTGTCTCCCAGTGA
Band lengths:
222-1480
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]