RnoINT0042629 @ rn6
Intron Retention
Gene
ENSRNOG00000030719 | Csmd1
Description
CUB and Sushi multiple domains 1 [Source:RGD Symbol;Acc:1305103]
Coordinates
chr16:78819953-78820847:+
Coord C1 exon
chr16:78819953-78820129
Coord A exon
chr16:78820130-78820667
Coord C2 exon
chr16:78820668-78820847
Length
538 bp
Sequences
Splice sites
5' ss Seq
CAAGTCAGT
5' ss Score
2.74
3' ss Seq
TCCTGCTCTCTACCCTTCAGTCA
3' ss Score
7.21
Exon sequences
Seq C1 exon
CCGTGTCCTGTGGAAACCCTGGCACCCCTACCAATGGGATGATCCTCAGCAGCGATGGAATCCTCTTCTCCAGCTCTGTCATCTATGCCTGCTGGGAAGGCTACAAGACCTCGGGGCTCATGACGCGGCACTGCACAGCGAACGGGACATGGACAGGCACAGCCCCTGACTGTACAA
Seq A exon
GTCAGTACCTACTCAGTTGGAAGCAGGGGTGGGGGTGCTGGAAACCTACCATTTGAGGGAGACAGTGAAAATCTAAAATCTATTGAATCTTTAAAAAGCATTCAGGATAAAGTATAACCTAAGTTTGATGTGATGCCCTGTTTCCTTAGATGCCTTAAGATCCTGCGTCTTTAATTTACACAACTAAAGTATGGACAGTTAGGCTATGTAATGAAGGAAGAACCATAGAGAAAGGTACAGATTCTCTGACTCTAGACCACCCAGGCTAAAAAGAAATAAGCTGCTTTGTTCTTGTCCATAGCTGTGGGTATATCCTGATCAGGCATGGCCAGGAGTGACAGCCAGTACTACCACCTATCAATATAGCAGTAATTAACAGTTCCAAACACAGTCACTTGGCAGCAGTTCAGTGGAATCTGTGCCCTGTGGCTGGTCCTTTCTTGGTTCCCTGCTGTATCCCAGAAGAGTGCTCACACAGTTTGGTTCCTGTCATGATAATTTTCATCCCTCTGGTTCTTTCCTGCTCTCTACCCTTCAG
Seq C2 exon
TCATCAGCTGTGGTGATCCTGGCACACTGCCCAATGGCATCCAGTTTGGGACAGACTTCACTTTCAACAAGACCGTGAGCTATCAGTGCAACCCTGGCTACCTGATGGAGCCCCCAACATCACCCACCATCCGCTGCACCAAAGATGGTACATGGAATCAGACCCGGCCCCTCTGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000030719:ENSRNOT00000057897:46
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=0.049
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=91.7)
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:
CGTGTCCTGTGGAAACCCTG
R:
GCCGGGTCTGATTCCATGTAC
Band lengths:
344-882
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]