RnoINT0033106 @ rn6
Intron Retention
Gene
ENSRNOG00000020129 | Cdh3
Description
cadherin 3 [Source:RGD Symbol;Acc:621089]
Coordinates
chr19:38706871-38709835:+
Coord C1 exon
chr19:38706871-38707095
Coord A exon
chr19:38707096-38709625
Coord C2 exon
chr19:38709626-38709835
Length
2530 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
AATAAATCATCTCTCTCCAGGAG
3' ss Score
7.85
Exon sequences
Seq C1 exon
GAAACCCTCCCACCACCGGCACTGGGACCCTCCTGCTAACACTTACTGACATCAATGACCATGGCCCAATCCCTGAACCTCGTCAGATCATCATCTGTAACCAAAGCCCCGTGCCTCAAGTGCTGAACATCACAGACAAGGACCTGTCCCCCAACTCCTCCCCTTTCCAGGCCCAGCTCACACATGATTCAGATATCTACTGGATGGCAGAAGTCAGCGAGAAAG
Seq A exon
GTAAGTCTGGTGATAAACAGGGGGCTGTCAGTTCAGCTGGGTAGGGGTCAGTCCCACAATAGGACTCACACACCTCCCTGTTCTAGTATCTGCAGGTCACAAAATTAGTGGTCTCAAAAATGGCCACCAGGTGTTTCCTTAGCATTATATGTCTTTGAAATTCCTCAGGAGCCCCTGTGGGGCTGGAGAGATGGCTCAGAGGTTAAGAGCACTGACTGCTCTTCCAGAGGTCCTAAGTTTAAATCCCAGCTCACGACCACTGTAATGGAATCTGATGCCCTCTTCTGGTGTGTCTGAAGACAGCTACAGTGTACTCATATACATAAATAAATGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAGTAAGTTCATTCCTCAGAAGCCCTAAACAGATAAACAGGGTTAGGTATGATTGCCTTAATCCCAGCACTCAGGAAGAAAAAAAAAAAAAAAGGTTTGTGGGTTCAAAGCCAACCTGATCTACTTAGTGAGATTTAGGGCTTTGTAATGAGACCCTGTCTCAAAAGAACAAGCAAACAACAACATCCACAATAAAAATGCAAGTTAAACAGAGAGAGATTTCTCAGAGGTTAAGAGCACTGGTTGGCCTTCCAGAGGACCCCGGTTCAATTCTCAGAACCCACATGGTGGCCACAACCTCCTGTAACTTAGTCCCAGGGGATCAGATGTTCTCTTCTGGTCTCTACAGCACTAGGTACACACGTGGTACACAGACATACATGCAGGTAAAACACCTGTATACATTAAATAGCATTTAAAATATTTTTTATAAAAGCAAAAAGCACGTTGCTCTTGTAGAAGAGCCAGGTTCGATTCCTAGCACCCACATGGTGACTCATAACTGTTTGTAACTCCCATGTCGAAAGATCTGACATCTTTTTTTGACATCCATAAGACATTAGGCACTCATTGTCCACATACAACATGCAGGCAAAACACTCATACCCATAGAATAAAATAAATGTTTGTTTAAAGATAAGCAACCGGGGTTGGGGATTTGGCTCAGTGGTAGAGCGCTTGCCTAGGAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCGAAAAAAAAAAAAAAGAAATTAAAGATAAGCAACCAAGTTAAATAATAATGTCTGTCTGTCTGTCTATCTGTCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTTCTTTTATTTGTTCGTTCTTTCTTACAACAGGGTCTCTGTGTATAGCCTTGGCTGTCCTGAAACTCACTCTGGACATCAGACTGACCTAGAACTCAGAGATCCACCTGCCTCTGCTTTCTGAGTTCTAGGATCAAAGGTTGTGTGCCACCACTGCCAGACTTATGATGCCTTTTTTAAAAATTTATTTATTTATTTTATATACATCATACAGTTTTCTGCCTGCATGTATGCCTGCAGACCAGAAGAGAGCATTGGATCACATTCTAGAGGATTGTGAACCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCGCTGAGCCATCTCTCCAGCCCCTATCATTGTTTTCTTGTTTGTTTGTTTTTAATAAAAGGACAGCCAAGTTCAGTGGCTCACACCTGTAATCCCAGCACTCAGAAGACCAAGGGAAGTGAATTAACATGAGTTTGAAACCAACCCAGACTACAAAGAACTCTGCCTGTAAAAGATTAAAAATAATGAATTGGACCTGGGCAGATGACTCAGTGGTTAAGAGCACTGGCTGCTCTTCCAGAGGACCCCAGGTTCAATTTCCAGCACCAACATGGTGGTTCACAAACTGTCTGTAACCACGGTTCCAGGGTATCCTACACCACATTCTTCTGGCGTCTAAGAGCACCAGGCATACGTGGTGCACAGACATGCAAACATACATGCAGACAAAACCCATACACACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATGTTGTGGTCTAGCAAGATTTCTCAGTAGACATAAGTGCAGCGCAGCTTGATGGAAGATAAGTTTGACCCTCAGAACCCAGAGGTTGAAGGAGAAAACTCATTCCAAAAAAGACTTGTTTTCTGATCTTTGTATGTTTATCATAGCACACACATGCCCACATTCTCACACACACACACACACACACACACACACACACACACACTCACACACCACAACAAAAACATAAGATGATATTTTCGAAAAAGAAAAGATACTAAAAGAATGAATTAATTCTGGTAACCCATTAATCCTTCTCACAGTGGTAAAGTTTTGCTCTGCCAGGGTTTTGGAGAGCTTCTGTTTGTTTTGCTCGTCTGTTTTGGGGATTGGGCCCAGGGCCTCGTGGACGCTGAACAGGTAGGTCCTCCATCACAATGCCACACCTAGACTAAACCTGCCTTTTGTTCTTTGGGTGCTGAGGCTGTTCTCAAACTTCTATCATCTTGTAGTCAGTGCTCAACCCGAATGACACCCCTAAGCTAATAAATCATCTCTCTCCAG
Seq C2 exon
GAGACACCGTGGCCTTGTCCCTGAAGAAGTTCCTGAAGCAAGACACATATGACTTGCACCTTTCTTTGTCTGACCATGGCAACCGGGAACAGCTAACCATGATCAGGGCCACTGTGTGTGACTGCCACGGCCAGGTGTTGAATGACTGCCCCAGACCCTGGAAAGGTGGCTTCATCCTCCCCGTCCTGGGTGCTGTCCTGGCTCTACTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020129:ENSRNOT00000027273:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.303 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(15.8=19.7),PF0002812=Cadherin=PU(54.5=63.2)
A:
NA
C2:
PF0002812=Cadherin=PD(44.3=54.9)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]