RnoINT0033103 @ rn6
Intron Retention
Gene
ENSRNOG00000020129 | Cdh3
Description
cadherin 3 [Source:RGD Symbol;Acc:621089]
Coordinates
chr19:38669230-38670282:+
Coord C1 exon
chr19:38669230-38669950
Coord A exon
chr19:38669951-38670164
Coord C2 exon
chr19:38670165-38670282
Length
214 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCA
5' ss Score
7.88
3' ss Seq
CCTTCTTCCCTCGCACTCAGGTT
3' ss Score
10.57
Exon sequences
Seq C1 exon
TTGTTCAGCTGCAAACGGAAGTAACTATTCTCTCAAACGTATATCAGATCCCTTACCGCGGTCCTTTGAGACCTCGATGCTACTTTTAAAACCCCAGTGCTTCCCCCGGGATAGTGTAGGAGGTGGAGAAAGTGGCAGAGGGCAGACCCCGCTATAGCTGGTGTAAAGACACGCCCTGCCTCCATCAAAGCTTTGAACACAAGCGCCTCCGGCAGCATGAATGAGGAGCCTCTGTTTTTTTGTCGGGTTTCAGATGAGTCTCCACTTTTTTTTTTTTTCCGCTGTAGCTGCCAGCAATGGAATATTTGTCTTCCCGTGCTGCAGAGGCAGAGGTGAAGTGGATTGGGGGTTTTGTTTTGTTACATTTGTTCCATTGAAGCCAGAAACTGCGAGAGCCACGGGGTACCTTTCAGAAGTAGTTCCAGAAGAGCAGGGAGGACGGAGGAGGGTACCGGGGAGGACCTTTAGGAGCTTCGGGAGCGACTTCGGCAAGCTGGTCTGGACTCCACCTGCGAGGGGGCGGGACCCTGTGACGTTTGACCAATCAGCAGCTACCTGAGCGCACCTGGCCTCCTCCCGCGGGCTCTAGCGAGCCGCGTTGCTCAAAGCTGCACCGGGAGCTTAGCGGAACGCTTGGCTACCGTCGCGGCAGCCTCCTCACCTCCCTTCAGTCATGGAGCTGCTTAGTGGGCCCCTGGTCTTCCTGCTCCTCCTGCTCCAG
Seq A exon
GTACCACAGTGCTTTGCTAATGGTCCTAACTCAGATTGCTCCCTGGAGGGCGGGTGGGGTTCTCACGCTGCGGGCGTCGGGGGAATCTTAGGGCTGTGCTCCTTGGGGCCAAGGTTGTCCCGGAGGCCCACCGAGGACTCCCAAGGATGGGTGTACAGAACCAGGCACGCTTGTGACTCAGCCTTCTCCTTAACCCTTCTTCCCTCGCACTCAG
Seq C2 exon
GTTTGCTGGCTACGCAGCGTGGTCTCCGAGTCCTACCGGGAGGACTTCATCCGGGAGGCTGGAGTGACCTTGGAGGTGGGAGGAACTGACCTGGAGCCGAGCCAAGCGCTAGAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020129:ENSRNOT00000027273:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.075
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACCCTGTGACGTTTGACCAA
R:
CTCCAGGTCAGTTCCTCCCAC
Band lengths:
294-508
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]