RnoINT0032863 @ rn6
Intron Retention
Gene
ENSRNOG00000020151 | Cdh1
Description
cadherin 1 [Source:RGD Symbol;Acc:69279]
Coordinates
chr19:38832633-38834037:+
Coord C1 exon
chr19:38832633-38832860
Coord A exon
chr19:38832861-38833906
Coord C2 exon
chr19:38833907-38834037
Length
1046 bp
Sequences
Splice sites
5' ss Seq
TGAGTAAGT
5' ss Score
8.82
3' ss Seq
CCTCCCTTCCCTGTCTCCAGTTC
3' ss Score
10.47
Exon sequences
Seq C1 exon
AACAAGAATCTCTCATTTTGCAACCAAGAAAGGACTTAGAGATTGGCGAATACAAAATCAATCTCAAGCTCTCGGATAACCAGAATAAAGACCAGGTGACCACGTTGGAGGTCCACGTGTGTGACTGTGAAGGGACCGTCAACAACTGCATGAAGGCGATCTCCCTGGAAGCAGGATTACAAGTTCCCGCCATCCTTGGAATCCTGGGAGGGATCCTGGCCCTCCTGA
Seq A exon
GTAAGTCCAGGTCGCAGGTGCCTCAAAACGGGGAAGGACCATCTGCTAAGAGGAGCTGGTAGTTGGAGTACAGAGCAAACTGGTGATGACGTGGAGTTGGGTGCGGGAGCCTTCTGTCTCTTTGTGCTCCCCTAGATTGAGGACATGCAAGTCACCTGTGCCCCTCAGTAAAGTGGGACTTTAGACCCAGCATTCCTAGCAGGACTCCGCAGAGGCTCCATTTTAAACCAGTCCCCAAGAAATGCTGAGCTGGCAGCAAGGGTATCGCACACTATTCTCGGTAGCATAGTTTAGCGGCCAGTTAACCACCCCCTCTGCATTCCATCCTGGAGGGCAGATGAAAGAGGAAGTAGAGGCCACCTAACTGCAAGTTGTAGATGTCGCCACCACTTGCATCTCGTTGGCTCAAATGTAGCCATACCAAGTTACAAGGAACCCTGGGAGCTCTTGCTCTTAACTGGGTGACGAGAGCCCATGGAATGTCTGGGAGGCAGTGGAGATGGAGGGTCAAGTGAACAATGGTATCTAATCCATGGCTGAAAAATTGAAAGAGAATGGAGATGCTGGAGGGAATCTGTCATTTCTGTCCATAGTCCTTGGTCTGATTTTACCTGGAGAGAGTTCTGGGCTTGGTGCCAATGCCGTGAGGATTTCAATGATCAAGGGTTTGTGGGGATTTTTCGTTTGTTTGCTTTGTTTTATTTTTTAATTGTTTATTGAGAACATACCTGACCTTTTTTTTTTAAATTTTTTTGGGGGGCAGTCGATATGTTTTATTAGACTTGGCTAAAGTGGAAATTCTCCTATCAGATGTTTGAAGCATAAGTGGTATCAGGAGCCAGACGTCACACTTGTTTATTATTTCTGTTGTATTGTTTCTTGAGAAATGGTCTCCTCTGACTGAACATGAGATAGTCTTCATTCAGGTGGCTACCCACCCGCCGCCTGCCTGGTGGTGTAAGACTGTGTGGTTCCGGGATGGCTGCTTCCTCTGCTTTCTTGCCTGTGACTCATCACTTTTCCCTCCCTCCCTTCCCTGTCTCCAG
Seq C2 exon
TTCTGATCCTCCTGCTCCTACTGTTTCTACGGAGGAGAACGGTGGTCAAAGAGCCCTTGCTGCCACCAGATGACGATACCCGGGACAATGTGTATTACTATGATGAAGAGGGAGGTGGAGAAGAAGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020151:ENSRNOT00000027346:13
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=0.364
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(44.9=51.9)
A:
NA
C2:
PF0104912=Cadherin_C=PU(22.3=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:
TCATTTTGCAACCAAGAAAGGACT
R:
TGGTCTTCTTCTCCACCTCCC
Band lengths:
346-1392
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]