RnoINT0042613 @ rn6
Intron Retention
Gene
ENSRNOG00000030719 | Csmd1
Description
CUB and Sushi multiple domains 1 [Source:RGD Symbol;Acc:1305103]
Coordinates
chr16:78745550-78747747:+
Coord C1 exon
chr16:78745550-78745727
Coord A exon
chr16:78745728-78747601
Coord C2 exon
chr16:78747602-78747747
Length
1874 bp
Sequences
Splice sites
5' ss Seq
GTGGTATGA
5' ss Score
5.27
3' ss Seq
TGGCCTCATCTTTTCCTCAGGGA
3' ss Score
9.65
Exon sequences
Seq C1 exon
CTCCCTGTGGGTATAATGTGACATCACAGAATGGCACCATTTATTCCCCTGGGTTCCCAGACGAGTATCCAATTCTGAAGGACTGCCTGTGGCTGGTCACTGTCCCTCCAGGACATGGAGTGTACATCAACTTCACCTTGCTGCAGACTGAGGCTGTAAATGACTACATCGCTGTGTG
Seq A exon
GTATGACTCCTCTCTCCCAGGGAATGGCAGCCCTTGATGGGGGTGGGATATGTTAGCTTAGATTTGCATGATCTTTCTGGGCAGATCTTGAAAAACTAATTGTCAACAAAAACAAACAATACAGAGGAAGATTTAAGGCATACGTCTAGTTTGCTATTAGATAGAAATAAACAGATTATTTGAATATATTAGGGAAAATTATGATTACTTTACTTCATATTCTGCTTTACTTAAATTATTGATAATTTTTTTAAATGTAAGATCTTACTCTGTGACTGAGGCTAGCCTTGAATTTGTGACCTTCTTGCCTCAGCCTCCTGAATGCTAAAATTGTTGCTGGGTGTCATTACGCCTGGCGTATTCCCCAGTTTTAAGGGATGTGTGTGCATGTGTGGGGGAAGGCTGTGTGTGTGTATTTGTGCGTGTGTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAAGGGCAGTATATACATATATGTACACATACACAGACATGTGTATGTATGTGTGTGTGTTTAAAGAAAAGCTATGATGTGCTTTCCCTTTAATGAATGCATGAACGAACCTTGAAGAAGTATTTTCTTGGGGCATGCCCAACCCTGGATTGCACAGGCCTGGTTTTCCTCAAGTCTGGCAGAGGAATATAGGCCAGGATGTGATGAATATGAATCTACTAGATGGACCCATAGAAATGACCTGATCCACCTTAGAGATCTCAGGTGCAATTTAAAGGGGAAGATGGCATGAGTACTCTCCCTTATAGTATGACAGAAGAGCCATAAGGTGCCCGTTGGGTACTAGGATGGTACCATTGTTAAATTTACAGATGGTGTACATTTGTGATGTATGATACGCGATATGTACATATTTATATGTACATGTCCCTGCATGTGTGGTGTATCCATGATTGTATTTGTGTTTATGAACATCCATGTTATATTGCATGTTTGTGTGTCTGTTTATAAATGAATACTTAGAGAATGCATGTATCTATACATCTCTGCTTGTGTCTGTAAATGAATGTATGATTGTCATATATGTACGTTGTATGTATCTGTATGTGAATGTATGAATGTTTTATGTTTATATATGTATTGGGTCTGTTTGTCATCTGTCTATTGAGTATCTAAGTATGTCTGCCTGTGTACGATATATGTATGCATGGAGGGTGTATCATGTGCTTGTTACAGCTCAAGGAGCAAGGGAGAGAGAGAGAAGCCTGGGCCAGAGGAACAGATACCACAGGGACTAAGTATTTTATCTAAAATATAGGAGGAACCATATACAGGAAAGTCACTGTGGATGATGCAGCAGAGCCCAGGGGAAGCTCCCTTCCCAGGCTGCAAGGAGGTCTTGCAGGGTAGTTCTGAGAAACTGATGTAGTGGCTGTGGAGATGAGACACCAAGAGTTCCTGTCCCAAAGCAGAGCAGCCAAGCAGCAGTCCCAACAAGCAATAGATCCATGTAGAATCTCTTGCATGGAATCTAGTTGTAGCAATTCAAGTATGTCCACTGCCCACAATCAGAAAGCAAATGAACGACAGAGATGCTACAGGAGAGTGAATGTCTTAAACACCAAGCATCCCATTACTAAATCAGTACCACGGCAAAACATGTTTCAATTTAAGTGTTTTAATTCAACTGTAAAACTTGTTATAAATGAGTTATAAGGAAGTGGACACTGTGTGTCCTTTAAAATGTAGTTGTTGGTTCCTGACAGCATAGAAGTACCTCTGAGGAAGTCAGTGTGCACTGGGATTCCTAGATCAGCTCCGTACTTTTTCTGCACCCTGGGCCCTATTGGGAAACTGGCTGTACAGCCTCATCTGTAACACCAAACTTCTCTCTCTGATGGCCTCATCTTTTCCTCAG
Seq C2 exon
GGATGGTCCTGACCAGAACTCGCCTCAGCTCGGGGTCTTCAGTGGAAACACTGCCCTCGAGACAGCATACAGCTCCACCAACCAGGTTCTGCTCAAATTCCACAGCGATTTCTCCAATGGAGGCTTCTTTGTCCTCAATTTTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000030719:ENSRNOT00000057897:31
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=0.020
Domain overlap (PFAM):
C1:
PF0043115=CUB=PU(54.8=95.0)
A:
NA
C2:
PF0043115=CUB=PD(44.2=92.0)
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:
CTCCCTGTGGGTATAATGTGACA
R:
AATTGAGGACAAAGAAGCCTCCA
Band lengths:
318-2192
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]