RnoINT0033109 @ rn6
Intron Retention
Gene
ENSRNOG00000020129 | Cdh3
Description
cadherin 3 [Source:RGD Symbol;Acc:621089]
Coordinates
chr19:38716653-38719677:+
Coord C1 exon
chr19:38716653-38716799
Coord A exon
chr19:38716800-38718947
Coord C2 exon
chr19:38718948-38719677
Length
2148 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
GCTGCTCTCTACTAACCTAGAAC
3' ss Score
4.95
Exon sequences
Seq C1 exon
GACTATGACATCACTCAACTCCACCGGGGACTAGAGGCCAGGCCTGAGGTGGTTCTCCGCAACGACGTGGCACCAACCTTCATCCCCACCCCCATGTACCGCCCCCGGCCCGCCAACCCAGATGAAATCGGCAACTTCATCATCGAG
Seq A exon
GTGAGGCATGACAGGTTTACTGAGCAAGACCAGCCCTGAGTCAGGCACAAGCATGGAGAACAAACACTGGCTTTCTGTATTGACTGTGAATTCTAATCCTGGCTCTGTCCTCCAACTATGCGATCTCTGCATACTCGAATATCTGTGGGTTTCTCTTTCCTCGTCCACAAACTCCAGATTTCATTATTGAGCTACTAGGAAAATACTCCAGAGTCAGGCAGCTTAGGTTTTATTTGGGGTTTGGGGGTTTAAGGTTCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTGTTGGTTTTTGTAGATTGTTTTTAATTTATTTTTTTTTATTTGTGTGTATGAGTGTTTTGCCTACATTCATGTTTGTAAACAACATGTGCACGGTGCCCTCAGAGGCCATAAGAGGGTGTTGGATTCCCTGGAACTGGAGTTGTAGACAGTTGTGAGCCCTGTCCTCTGGAAGAGTAGCTGAGACTCTTGGCTGCTGAGTTTGTAAACAACATGTGCACGGTGCCCTCAGAGGCCATAAGAGGGTGTTGGATTCCCTGGAACTGGAGTTGTAGACAGTTGTGAGCCCTGTCCTCTGGAAGAGTAGCTGAGACTCTTGGCTGCTGAGCCATCTCTCCAGCCTCTGCTTTGCTTTGCTTGTTTGTTTGTTTGTTTGTTTGTGACAGGGTTTCTCTGTGTAGCCCTGGATGTTCTGGACCAGGCTCTCTGTAGACAAGGTTGGCCTCAAACTCGCAGAGACTCTCCGGTCTCTACCTTCCAAGTGCTGCAATCAATGGTGTATGATACTATTCCTGGCCTCTTGGGGGTGTTTATTTCATGTTTTTACGTTTTATATATGTTTTTAGTGTCTGTCTTCCATATCTGTCATGGTACACAAGTGAGGGTCAGAGGACAAGTTTTTAAGTTTTCATTTTATTTTCTGTTGGTGTATGTGGAGCTGGAGAGATGGCTCAACAGTTAAAAAGTATTTGCTGCTCTTCTAGAGGACTGGGGCTTGAATCTAAAAACCCACGGAGACTGACAGCATTCTGTAACTTCAGTTCTAGGGGTATCCAGTGCCCTCTTCTGGACTTTGCAGGCACTGCATACACATGGTGCATAGACACGTGCAGACAAAACACCAATGCACATAAAATAGATAAACCTTTTTTTTTTTAAAGATAAACCTTTTTTTTTTTTTTTGGTTCTTTTTTTTTGGAGCTGGGGACCGAACCCAGGGCCTTGCGCTTCCTAGGTAAGCGCTCTGCCACTGAGCTAAATCCCCAGCCCCTAAGATAAACCTTTTAAAAATAAAAGTAATTTTTAGGCCAGGCTTGGTGGCACACAACTTTAATTCCAGCATTCAGAAGGCAGAGGCAGGTGGATCCTTGTGAGTTTGAGGACAGCCTGGTCTACAGAGCAAGTTCCAGGACAGCCAAGGCTACACAGAGAAGCCCTGTCTCGAACCCCTCCAAATAATAATAACAGTAATAATAACAACAATAATTTTTAAAAGTTCGTGTAGTAGTATATGTCTTTAGTACCAGAATTTAATAGGCAAAAGCAAGCAGATCTCTGAGTTCAACACCAGCCTGGCCTACAGAGTAAGTTCCAGAACAGCCAGGGCTTCATAGGGAGACCCTGTCTCAAAAAAGAAAACAAAACAAACAAACAAAAAAAAAAACAAAATGATAATAGTTTTTTTTTTTAAATTAAGTACTGGACTGCTCTTCCAGAAGTCCTGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAGCCATCTGTAATGGGGATCTGATGCCCTCTTCTGGTGTGTCTGAAGACAGCTACAGTGTATTCACATATACTAAATAAAGTCTTTTTTTTTTTTCTTTTTTCTTTTTTTCGGAGCTGGGGACCGAACCCAGGGCCTTGCGCTCGCTAAACGAGCGCTCTACCGCTGAGCTAAATCCCCAACCCCCTAAATAAAGTCTTAAAAAACAAAAATAATTAAGTGCATGTATCTAGGGAGGAAAGTGTCCATGTGGAGCTAGGGGGTGGGTCCACGTGGGGGTAGGGATGGGTATAGAGGCTCAGCAGGAGTACTGATTTGTCAGAACCCAGGCAGCTGGCAAGGGTCTCCATCCAATGTGTGCTGACTGCTGCTCTCTACTAACCTAG
Seq C2 exon
AACCTGAAAGCTGCCAACACAGACCCCACTGCTCCTCCCTACGACTCCCTGCTGGTGTTTGACTACGAGGGCAGTGGCTCTGATGCTGCCTCCCTGAGCTCCCTCACCTCCTCCACCTCTGATCAGGACCAGGACTACAACTACCTTACCGAGTGGGGAAGTCGATTCAAGAAACTGGCTGACATGTATGGTGGCGGTGAGGATGACTAGACTGGCCGGCCATGCTGTCCAGGCAAGAACTACAGACAGGTCACAGCAGCATCTCAGGGGAGCTCTCACTCCTGCTCCTGAGGACTCTGAAGCTCGCCAGGAAGTCGCCCGCAAAGCAGGCTGCATCTGACATGAAGGCTAGACTGTGAGCCTTTCAAATGGGAGGATGTGACTCTGACTTCAACACTGATCCCCCTCAGCCGATGCTGAGCCCTCAGAATGGACTGTCTAGAGGTCTCCCGCCTGCCACACAGGGCTCAGGGCAGAACTTGCTCTGATGCCCTTGGTGACTTTCTCCACTTGAATGGCTCTCTCTTTAGAAAGAGACCTCTCACTAAGGCCCCTTTTTCCTTTAATGCAGTTTTCATAAAGAGGCTCAGGGTGGGGCAGGGTGCAGACATCAGTCTCCCTTCAGGCCCTCCAGAAGAGAAGCCTACAGGGCACTGGCCCTGGTACATTTCTCTGATCTCCAGGTCTTGAGGCCTCACATTGGGAGGGATAAATGCTTTTTTTTTTTTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020129:ENSRNOT00000027273:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.286 A=NA C2=0.377
Domain overlap (PFAM):
C1:
PF0104912=Cadherin_C=FE(32.0=100)
A:
NA
C2:
PF0104912=Cadherin_C=PD(43.3=92.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
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]