RnoINT0042639 @ rn6
Intron Retention
Gene
ENSRNOG00000030719 | Csmd1
Description
CUB and Sushi multiple domains 1 [Source:RGD Symbol;Acc:1305103]
Coordinates
chr16:78838533-78839479:+
Coord C1 exon
chr16:78838533-78838645
Coord A exon
chr16:78838646-78839391
Coord C2 exon
chr16:78839392-78839479
Length
746 bp
Sequences
Splice sites
5' ss Seq
TATGTAAGT
5' ss Score
6.69
3' ss Seq
CCCCTTTCCCTGCACACCAGGTA
3' ss Score
7.66
Exon sequences
Seq C1 exon
GGGTCTACAAGAAGGAAGAGGCCCACCTGCTTCTGAAAGCCTTTCATATCAAAGGCCCAGCAGATATTTTTGTAAGCAAGTTTGAAAATGACAACTGGGGACTCGATGGTTAT
Seq A exon
GTAAGTACTTCCATGAAGATTTTTCATATGGTCCTCCCGCTTTCAGGTCTGGGCAAAAGAATTCATGATCCACTGAGAATTATGGGCAGAGGAAACACTGCCCATCCCTCAGGAACTCAGAAGGTACCCCTGAAGCAAGGTCACAGTATCCCATCATTTGATAGAGGCAACCACCAAATCTCTGATATAAGAAAAGAGTTGGCCCAGAGTTAAGGGAATTCTTCCTGCTGAAGACAACCAGGTTCTTCAGTCTAGGTTAGACTACGCTAATCCACACCCTCACTGTCAGGGTTGTGAACATTTAGAGATCAGCTACACAATACTCAGAAGGCTCCTCAGAGTACAGAAGAAGCTGGTGCAGTGTCTTTCTCTGCGAGTTAGGCAGCTTCTGTGGCCCACTTTGCTATGACAATGTTTCACAGTCTTACATGATGTTCACCGGGATGGAGCCAATGAAAGTGAGTCCACGGAACATAGTGTTCCCCATTTGGGAAGGTCATTGCCATGTGACCCTTTAGAATGGATGATCATGTTAGGAATCAAGCTGTCTGTCATCATGACGCTTCCTATGGTGCTCGACCTTTAACTCAGTACTGATTTTCAGTTTACTTATGTCAGTAAAATGAGTTGGGGAAAATTCCACTCTGGGCATGCAATGTCTAAATCTGAGTGTTGACAGTTATCTTTGGGTGACAGCTACATTTTCTCTCCTTCTTATGCCTTGCCCCCCTTTCCCTGCACACCAG
Seq C2 exon
GTATCCTCAGGACTTGAGAGAGGAGGATTCTCCTTTCAGGGTGATATACATGGAAAAGACTTCGGGAAGTTCAAGCTGGAAAGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000030719:ENSRNOT00000057897:55
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=0.100
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GGTCTACAAGAAGGAAGAGGCC
R:
TGTCTTTCCAGCTTGAACTTCCC
Band lengths:
198-944
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]