RnoINT0042614 @ rn6
Intron Retention
Gene
ENSRNOG00000030719 | Csmd1
Description
CUB and Sushi multiple domains 1 [Source:RGD Symbol;Acc:1305103]
Coordinates
chr16:78747602-78748442:+
Coord C1 exon
chr16:78747602-78747747
Coord A exon
chr16:78747748-78748361
Coord C2 exon
chr16:78748362-78748442
Length
614 bp
Sequences
Splice sites
5' ss Seq
ATGGTCAGT
5' ss Score
6.57
3' ss Seq
TTTTCATCAATATACTACAGCAT
3' ss Score
4.81
Exon sequences
Seq C1 exon
GGATGGTCCTGACCAGAACTCGCCTCAGCTCGGGGTCTTCAGTGGAAACACTGCCCTCGAGACAGCATACAGCTCCACCAACCAGGTTCTGCTCAAATTCCACAGCGATTTCTCCAATGGAGGCTTCTTTGTCCTCAATTTTCATG
Seq A exon
GTCAGTTTGTTTCTATTTCAGTGAATGTGACATAGAGTCCCAGGAAAGCTCTCTACCCCATGTACATACTTTATCTCCAGCTGTTGAATTATCCCACGTGGATGACAGGTGTCCTGGAATGCTTTTGTGGTGGGCAATATCTCTGTTGTCAGTTCACTTCATCAGGTCATGTTGGTAGATACCTAGGGTTCATTCCTACATAGATAGAAGAGAGACTGTGTTGTAGACACCATCATGATGCACATGATGTCTAAGGAAATGTCATAGTAACCATCATATAATGACCTCATGATGTCCTTTTTAGCAAAGGGCAAGGTCATCAACCCCTTGTCACTTATGACCCCCCAAATGTTACTCAGGACCAGAGAGAAATGAGCTTATCTAAACAGGCAGGCTGTGGTGGGAGGATTTCAGTGGTGTCTTCCAAAAGGGGGATGATAGGTGTCATAGTAGGAACTGCATGTTTTCATCCCTTGAGCTTCAGGTATTGTCAGACATTTAATAGCCATAGTGAGTCACTGGAGAGAGTGATTTACATATGCACATGGCCTTGTAATTTGATCATTCAGAAGAGGTAACCACAGCTGTTATCATTTTTCATCAATATACTACAG
Seq C2 exon
CATTTCAGCTGAAGAGGTGCCCGCCTCCTCCAGTAGTGCCGCAGGCTGACCTGCTCACAGAAGATGAAGACTTTGAAATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000030719:ENSRNOT00000057897:32
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043115=CUB=PD(44.2=92.0)
A:
NA
C2:
PF0008415=Sushi=PU(36.2=75.0)
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:
GTCCTGACCAGAACTCGCCTC
R:
AAGTCTTCATCTTCTGTGAGCAGG
Band lengths:
214-828
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]