RnoINT0042635 @ rn6
Intron Retention
Gene
ENSRNOG00000030719 | Csmd1
Description
CUB and Sushi multiple domains 1 [Source:RGD Symbol;Acc:1305103]
Coordinates
chr16:78829466-78831506:+
Coord C1 exon
chr16:78829466-78829577
Coord A exon
chr16:78829578-78831326
Coord C2 exon
chr16:78831327-78831506
Length
1749 bp
Sequences
Splice sites
5' ss Seq
TCCGTAAGT
5' ss Score
10.27
3' ss Seq
TGGACTAAATGCCTTTTCAGCCC
3' ss Score
4.34
Exon sequences
Seq C1 exon
GTTGGAAGCACTGTGTTCTTCAGATGTAGAAAAGGTTACCACATCCAAGGCTCCACTACCCGGACCTGTCTTGCCAACCTCACGTGGAGTGGAATCCAGACAGAGTGCATCC
Seq A exon
GTAAGTCCCCGTTCTTCCTTCACAGACTCAACCCCAAGTATCCGCAAAGAGCTCACCTGCCGGGGAAGCTGGGAAGAGAAGTGGGGTTGTTTATTTTTTCATTCTCTAACTCCAAATTTGTGCATCTCTCAAAATGGTCCTAAGGTTCTTAGATGAGTCAAACCAACAAGGCTGAGGGCTTGGGGAGCGATGATGATCTTCAACCCCAAGAACTGATGTGTTAGAAACTGCTTGGTAGGAAGCAGGATGAGGCACCAGGTGACAGGAAACTAGGTTCTCAGGGGATGTGAGGCAAATGCCAGAAACGCAAAACAAGAAATGATGTCAGATTCAGCACTGTTGGGCAGAAGGTCCCGAGTACTTGGCCATCCTTCTGTGTGTTTATACTCCATTTCCTGAATCCAGGAATGAGCAGGAGACAGCGTGTGAACTCAGCGTGATAGTGTCACCATAGACATTGGACAGTGATGGATGGAGTAGATTTTACTTTGTGATTCAATCATGAGAACGTGCTGTAAGGAATTTGAACTAAGTGATTCATATCACCCACTGTTTATATTAGACAACCCTGTGCCTTGCTATGGTGAACAGAAAAGTTATCCGCAGAATGCTGTGGAAAGTTATTGTAAGGATGAGTAAAATAGAAGTTATCATGGTTTTTTATCAGATTAATCATGTGTGCACTTATGTCAAAGCTGACATAGCTACCTCACTACTCAGTCATGTGGAGAAGCTATGCACATATGTGTGTACAGTCATGTACCCACACACTAAGGCATGGATATGTGTATTATGAACCTTGCTATAGTACAGGAAAAAAGGTTGGAAATTTGCTAAATTATGAACTATTGACAATGCTTAAAACAACTAAATTCACAACTGTGAACTTGCTGGCTTGTTTAATGACCATTTTCTAAGTCCTGAACTGAAGACATGTGTGTGTTTTATAAAACAAGATTATTTGTGGTAGCACATGAGTATTCAAATTTTATTCCTCCCCAAATTATATCTTTAAAGGAAATAAGGACTTACAATTCTATAAATAAACCTCTAAAACATGCCAAAATTTAACATTCATTTAGTTATACAATAAATATATATGATGTCACCCGACAAGCATATATCTGAATATGCACGGGTTCACATATGTTAGCTCATTTGTATTATCAGTTATTAAAGGTTTTTTAAAGTGTTTATTTTCATTCTTATTTGTGCATGTCTATATGAGTATGTGCACATATATGTGATTATGCACAGAGACTAGATGAAGGCCCCAGATCCCTGGAGCTGGATTACTAGTAAGTTGTAAGCCATCTAACATGAGTGCTGGCAGCAACTCAAGTCCTCTGGAAAAGTGGAAACTACTCTAAAACACCTAGCTATCTCTCCAGCCCCACATTAAGAAATAATATATTATTTCTCTTGTGTTATGCCTCTGTCTTTTAGTCAAAACTAGGATCTGTCCTCTAAATTTATATATATATATATATATATATATATATATATATATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTGTGTGTGTACGTATGTATACATATTACATATGAGTATGTATATACATAAATGTATATATATGTACACATTTCTCACATATGTAATCCCTAACTTCATAACCTTTAGTAGATGTTTCCTTCATTAGTTCCTATGGACATTTGAAAGGTAGTAGCTTTACAACAAAGACCCCCATTGCTTTTTAATGGACTAAATGCCTTTTCAG
Seq C2 exon
CCCATGCCTGCCGGCAGCCAGAGACCCCAGCGCATGCAGATGTGAGAGCCATCGATCTTCCAGCTTTTGGCTACACCTTAGTCTACACCTGTCATCCAGGATTTTTCCTTGCTGGCGGATCTGAGCACAGGACGTGTAAAGCAGACATGAAATGGACAGGAAAGTCACCTGTTTGTAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000030719:ENSRNOT00000057897:51
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:
PF0008415=Sushi=PD(63.6=92.1)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.8)
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:
TGGAAGCACTGTGTTCTTCAGA
R:
CAGGTGACTTTCCTGTCCATTTCA
Band lengths:
281-2030
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]