RnoINT0042631 @ rn6
Intron Retention
Gene
ENSRNOG00000030719 | Csmd1
Description
CUB and Sushi multiple domains 1 [Source:RGD Symbol;Acc:1305103]
Coordinates
chr16:78823353-78824302:+
Coord C1 exon
chr16:78823353-78823526
Coord A exon
chr16:78823527-78824128
Coord C2 exon
chr16:78824129-78824302
Length
602 bp
Sequences
Splice sites
5' ss Seq
TGCGTAAGT
5' ss Score
9.73
3' ss Seq
AGGCCTGTTTATTTCCCCAGCTG
3' ss Score
6.27
Exon sequences
Seq C1 exon
CTGTTCTATGCAGCCAGCCTCCCTCAGTGCCAAACGGAAAGGTGGAGGGGTCAGACTTCCGATGGGGTGCCAGCATAAGCTACAGTTGTGTGGATGGCTACCAGCTCTCCCACTCGGCCATCCTGTCCTGTGAAGGGCGTGGAGTATGGAAAGGAGAAGTCCCTCAGTGCTTGC
Seq A exon
GTAAGTCATGTGGTAGAACCTGTCCTGTGATCCTGGACACTCAAAGAGGCACTCCCAGCAGCCTAGTGACGTGTGACTGTGGTCAAATTGTATAAACTCTGAGATCTGAGCATGTGTGGCCAAAGGCAGGTGCTGCTATGAGTTTGTGGTGGTTCAGAGGTTCACCAGTCTGACCATTAATAAAATTAACCATTAACAAAGAAGAAACATCTGTTCAGATCCTCAATCCACAGCCACATACCCTGGGCCAGCCACTTCAGTCAGGGGTTTATAAAAACAAATAATACAAAGTGACAACTTGTTTTCACAAGCAGAAGATCAGAATGGTGCATAGCTTTTTACAGAAGCAGAACAGGGCAGTAAAAACTTTTACCCTTAATATTCCTTAATAGTTGGAGGTCTAATTTTGCTTCGTGGTTCTCTTAAGCACAGAGAATTTAAACCTAAAACATAAAGTTAGCCATCAACATTATGTTAGCTATCACTGTGCCTTCTCCTTAGGAGTGTGCATAATCTCAAGACTCCATAGGATCTAAACAGGTTTAATAGGCTAGCCTGGTTCAGACAAGCTGAGTGCTGATCAGGCCTGTTTATTTCCCCAG
Seq C2 exon
CTGTGTTCTGTGGCGATCCAGGCACTCCAGCAGAGGGACGGCTCAGTGGGAAAAGCTTCACCTTTAAGTCTGAGGTCTTCATCCAGTGCAAACCCCCATTTGTGTTAGTGGGTTCCTCGAGGAGAACCTGCCAGGCCGATGGGATGTGGAGTGGCATCCAGCCCACTTGTATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000030719:ENSRNOT00000057897:48
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.017 A=NA C2=0.017
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=91.5)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.5)
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:
CTGTTCTATGCAGCCAGCCTC
R:
CTATACAAGTGGGCTGGATGC
Band lengths:
348-950
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]