RnoINT0140948 @ rn6
Intron Retention
Gene
ENSRNOG00000023548 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:RGD Symbol;Acc:1566079]
Coordinates
chr9:100400831-100403099:+
Coord C1 exon
chr9:100400831-100400993
Coord A exon
chr9:100400994-100402973
Coord C2 exon
chr9:100402974-100403099
Length
1980 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
GCTCCTTCCTGTGTCCACAGCCT
3' ss Score
9.47
Exon sequences
Seq C1 exon
GCAGGTTTCAACGCAGGTGATGGGCACCGCTACTTCAACATCCCTGGGTCGCGCACAGCAGACATGGCTGAGGTGGAGACCACCACCAACGTGGGCGTGCCCGGGCGCTGGGCGTTTAGAATCGATGATGCCCAGGTGCGCGTGGGGGGCTGCGGCCATACAA
Seq A exon
GTAAGAGGCTCAGGGAGGGGAGGGTTGAGGAACCCTGTGGCAGTAGGGGTGGGGCAGAGGGGCTAGAACCTATCCACCACCTCACTGAATTTCCCACCTACCCCCCCCACAGTCCATCCCGTCCCATGCCTCAGGTGACCTAGGTCTTTTGGGGAGAGGAAGGGAGCAGGGTTGCCACATCCCACCCCTGCCTCCATCTGTGGTGGGTGTTGGGGGGACAAGGACATCCATAGGCCTGATGTTGGTGACAAGCCAGAGCATTTTATGGTCTTGCTGGTCTAGGAGCACAAACAGGCAGATGACTCCAGTAGCCCAGACTAGTCATGTGCTCACTCAGAAACCCCAGCTCCACTGCCATGACTCCTCTAGAAGGTACCACACCCTGAAACACCCTGCCCACAGTGCAGAGGTGTCCGGGCACTGGCTGGCTGACCTGCCAATTAGGAGGACCCCCCTCATCGCAAGCCCTCCTAAACCTGGGTTGAAGACAGGCCGCTGCTGGGACCATCCCACAGTCTTGTTGCTCATGTGAATGAGGCCACAGAACAGGGTGCCCTTCCCTGACACCGAGTCCCCCCCAAGAGAAGTCAGCAGGGATACCACACAGAGCTGCTGAGAGTCAGGGAGGCTGTCTGGTGAAGGGAGATTAGGGTGTGAAATACCAGGGAGGGAGAAGCTGGAACATGCCTGGCACGCTGGGTACTGAGAGCCACGTGACGGGCCAGCCTGGGAAGCCAAAGCTGAACTCAATGCCATCACGGACCAGAGCAGCAAGTGTAGCATTTAAGAGGGCAGAATCCCAGGGCAGCCCTAGCCCCAGTCCTGGCCATCAGTCAGCCCTGACACCAAGTCTCCGGGCCATAGCATCTGAAGCCGTCCTGCAGGTGCCACTTGTGGTGGGGACTGGGGGTCCCTTGTCAAAGGCCAGAGTGCTAGGTTCTGGTGAGAATGGAGGTACATGTGTGGGCAAACCATACTTTGAAGCCACAGCAGCTCAAGTCGAAAGGCACTCTGGGAAGAGGATCCCTTTGGGGCGCCATCATTACGGAGCACCTTTATCCGGGTCTCTGAGATAAGAAGGCACAGGAAATGGCTGCAGGGATATGCCTTGGTGCCTGTGGTCTTTCTAGGAGCGAGGGACACAGCTAAACTGCATGCCAAGGGCAGTTGTGGGACATTATATAGACACAAGCTTGCTCAAGAAGGGAGGGTGGGTGGTGCCTGAGAAACGGTCAGTGCCTTGTGTCTGGAAGGGTAACTACCAAGCAAGCCCAGCTCCTCTTGCAGCCAAGATTTCAAGTAGACCAGGTGAGCACAGTGCTGTAAGTGAAGCCAGCTGACAGGATGCTAAGCTCCCCATCCAGAAGGCACCCACAGTCTGAATGGTGTGCTGGATCACTGGGCCTCTCTGGAGTCTCCCTGGAGCCCTACTGAGAGCAGGCAATAGGAGTCCTTGAGACTTTCTGATCACCTGCCAATTTGTTAGTAACCTCTTATTTCAGGAGCCCAGCCTGGCCTCGTAGAACTGGGCTTGGGGGTTGCTGAGATCTCCAGAGACCCTAGGGAGGCATGATAACCACTGGCTGTGATGATGAAGTGCCAACTTAGGAGACCAGGAGGGTGGCTGAGCAGGCCCGAGCTTCTAGAAGTGTCCATGGTAGAAGTGGAAAGGATTAGAAAGATAAAAGAAGGAGCTGTGGGTGTATGTGATTGTGGGTGTGTCTGCCACCAGAGGAAGCCAGAGTCAGAACTTAGGACACTAAAGATCAGCAAGAGATCCTGGCAAGAGTACCTGCCAGGCAAACAGGGCTCCAGCTCAAAGACCCAGAACGTGAGCGCAAAGAAGCATGGTCACCAGTGTTGTAGTCACTAAACTGTCCTTTGGGCAGAGAGAAGGGAGACGCGGCCATTGCAGGTGGCTCTCTTGCCCACATCCTAGATGCAGTGTTATGAGGCGTGGGCTCCTTCCTGTGTCCACAG
Seq C2 exon
CCTCTGTGTGCCTAGTCCTGCGTCCGTGCCTCAATGGTGGCAAGTGCATCGATGACTGTGTCACGGGCAATCCCTCCTACACCTGTTCCTGTCTCGCTGGCTTCACGGGGCGTAGATGCCACCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023548:ENSRNOT00000022290:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.055 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF061199=NIDO=PD(47.3=78.2)
A:
NA
C2:
PF0000822=EGF=WD(100=83.7)
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:
AGGTTTCAACGCAGGTGATGG
R:
CATCTACGCCCCGTGAAGC
Band lengths:
279-2259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]