RnoINT0032862 @ rn6
Intron Retention
Gene
ENSRNOG00000020151 | Cdh1
Description
cadherin 1 [Source:RGD Symbol;Acc:69279]
Coordinates
chr19:38832144-38832860:+
Coord C1 exon
chr19:38832144-38832368
Coord A exon
chr19:38832369-38832632
Coord C2 exon
chr19:38832633-38832860
Length
264 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGA
5' ss Score
5.29
3' ss Seq
TTTTTTTTTCCTTTCCCCAGAAC
3' ss Score
12.05
Exon sequences
Seq C1 exon
GTTCACCCATTGCCACTGGCACAGGGACTCTTCTCCTGGTCCTGTCAGACGTCAACGACAATGCTCCCATCCCAGAACCTCGAAATATGCAGTTCTGCCAGAGAAACCCGAAGCCCCATGTCATCACCATCTTGGATCCAGACCTTCCCCCAAACACATCCCCCTTCACTGCAGAGCTCACCCATGGGGCCAGCGTCAACTGGACCATTGAGTACAATGACGCAG
Seq A exon
GTGTGAAGGCTCACTGTTTTTAGAGAGGTTCTACCAGTCCCGCTTCACCCTTCCCTTTGATATTCGGCCCTAGTTCCTTACACATCTCATGCACACTCCTATTCCTCTGAGAGACATACTGCACAGTAATATGAGCTCCAAACAGTTCCTTCCCCCAGCACTGGATGCCCAGCACTTTGGTTCCCTAAACATTTTGATCCACTGAGCTATTCATTCTGTCCCCTCCCCTGGTTCCATCGTTTCTTTTTTTTTTCCTTTCCCCAG
Seq C2 exon
AACAAGAATCTCTCATTTTGCAACCAAGAAAGGACTTAGAGATTGGCGAATACAAAATCAATCTCAAGCTCTCGGATAACCAGAATAAAGACCAGGTGACCACGTTGGAGGTCCACGTGTGTGACTGTGAAGGGACCGTCAACAACTGCATGAAGGCGATCTCCCTGGAAGCAGGATTACAAGTTCCCGCCATCCTTGGAATCCTGGGAGGGATCCTGGCCCTCCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020151:ENSRNOT00000027346:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.263 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(14.7=18.4),PF0002812=Cadherin=PU(53.9=63.2)
A:
NA
C2:
PF0002812=Cadherin=PD(44.9=51.9)
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:
ATCCAGACCTTCCCCCAAACA
R:
CCCTCCCAGGATTCCAAGGAT
Band lengths:
302-566
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]