RnoINT0033120 @ rn6
Intron Retention
Gene
ENSRNOG00000052405 | Cdh4
Description
cadherin 4 [Source:NCBI gene;Acc:114588]
Coordinates
chr3:175272532-175274855:+
Coord C1 exon
chr3:175272532-175272765
Coord A exon
chr3:175272766-175274621
Coord C2 exon
chr3:175274622-175274855
Length
1856 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
GTTGCTGTTTTTCATTCCAGGTG
3' ss Score
10.31
Exon sequences
Seq C1 exon
GGATCCCCCCAGCCAGTGGCACTGGGACCCTGCAGCTCTACCTCATCGATATCAATGACAACGCACCACAGCTGCTGCCCAAGGAGGCACAGATCTGCGAGAGGCCTGGCCTCAACGCCATCAACATCACCGCAGCCGACGCCGATATGGACCCCAACATCGGCCCTTACGTCTTTGAGTTGCCCTTCATCCCCACTACGGTGAGGAAGAATTGGACCATCACCCGCCTAAATG
Seq A exon
GTGAGTCCACCCAGCAGTGCCCTAGCCACCAGCAGAACCAGTATCTAAGGATCTAGGATTCCATCACTGAGAAACAGTGAGCTACGGAGCTGGGAGACAGTCCTCGCCTTCCGCATGGTTCACACACAAGGCTGGAGATACAGCCCTGTTTATCTGTGCCTCCACCACAAGGCTGTCTTTGCTCCTAGCGCCTCCCTGTTCTAGAAAGAGCCTAGCTCGACCATGCTGGCAACCGTTGACCGTCGTCTGTAGCCCCTGGAGAACGCACCCCTTAGGAGGCACCGGCTGCGGTGATGTTGATGGCATTGAGGCCGGGCCTCTCGCAGATCTGTGCCTCCTGTGTGGCCAGTGCTAGGAGCCTTACACCTTCCTAGAGATGCGATGCCTGTTTATGGTTCCACCAGCAAAACTGCCGATTCTTCGGGCCCATGGCAACATAAGCCCGATAAGCAAAGCCACCGCTGTCCTCTGCCCCTGGGCTCCTGGTGGAGAGCGTTCCCATGCTCACTGAGGTGTGGGTTCCTCTCAATGACTTTGCCTTTCAGGAGAGTTGGGTTTTGGAGGTTTTTGTTTTGTTTTGTTTTTCTTTTTGTTTTTAAAGATGTATTTATTTCATGTATGTGAGTACACCGTACCTGTCTTCAGACACACTAGAAGAGGGCATCGGATCCCATTACAGATAGTATGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTAACCGCTGAGCCATCTCTCCAGTGCAGGTGGTTTTGGTTTTTTTTTTTTGTTGTTGTTGTTTGCTTGTTTTTGCTTTTGTTTTTGTTTTTGTTTTCTCCTAATTGATTTTATAGAACTCTATACATTCAGGAAATCATTTCTTCACCCTAAATACTGACTCACTTTTGGTCCTGATATGGTTGATGTTTTAGCTTTGTGTGTCACTGTATGTGTGCAGGCACACATATGTTCAGATACATGTGTGTGTGCACAGCAGGTCACCGTCAAGCTCTGCTCTTGATCCTTGGGAGATGTCCACCCTTTATTTTTTTTCAGACAGGGCCTCTCTGGCTGGTCAGCCAGCTCCAAAACTCTGCCTGCTTCTGCCTCCCCAGATCTGACTATAAGTATGCACTCTGTAGCAGGCATTTTAGATGGGGTCCAGGGAGGTACAGTTCAGATCCTTATGCTCGTGTGATAAGAGCTTGACCAATGGAACTATCTCTCAATATCTTTAACTTAATGGCGGTAGAGTGTGCGTGTGTATGTGTGTGTGTGTGTGTGTGTCTGTATGTGTGTGCCTATATACATATGTGTACACACACATCTGTATGGTGTGGTGTGATGTGTGTGCATATATGTACATTGTGTGCATGATGTATGTACATACACATGTGTATGCGTGTGTGTGTACGTGCATGGCATGTTGTGATGTGTGTGCATATGTGTACATCATGTACATGATGTATTACATGTATATGTGTCTACATGTGTACATATGTGTGCATGATGTGTGTGCAGGGACGTCTATATGGTATGTTGTGATGTGTGGTGTATGTGTGCATATGTGTACACTGTGTGCATGATGTATGTATGTGCACATGTGTGTGAGACTGCATGGTATATTGTGATGTGTATGCATGTGTGTACATTGTGTGTATGATGTACATGCATGCATGCACGCACGCACAGGCGCACGTGTGTGTGTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCTTTTCATGCCATCAATCTCAGTGCCTGCGGAGGTCTTCCTTGGGAAGGATAGCTGCCGACTGGCTGCACGTTGCTGTTTTTCATTCCAG
Seq C2 exon
GTGACTATGCCCAGCTCAGTTTGCGCATTCTGTACCTGGAAGCAGGGGTGTATGACGTCCCCATCATTGTCACGGACTCTGGCAACCCTCCCCTGTCCAACACATCCGTCATAAAGGTCAAGGTGTGCCCGTGCGATGAGAATGGCGACTGTACCACGGTCGGTGCAGTGGCTGCAGCTGGCCTGGGCACGGGCGCCATCGTGGCGATCCTCATCTGCATCGTGATCCTGCTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000052405:ENSRNOT00000088026:11
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=0.000
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(15.8=19.0),PF0002812=Cadherin=PU(54.3=64.6)
A:
NA
C2:
PF0002812=Cadherin=PD(44.7=53.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTCAACGCCATCAACATCA
R:
CAGATGAGGATCGCCACGATG
Band lengths:
343-2199
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]