HsaINT0032168 @ hg19
Intron Retention
Gene
ENSG00000062038 | CDH3
Description
cadherin 3, type 1, P-cadherin (placental) [Source:HGNC Symbol;Acc:1762]
Coordinates
chr16:68678151-68679653:+
Coord C1 exon
chr16:68678151-68679327
Coord A exon
chr16:68679328-68679538
Coord C2 exon
chr16:68679539-68679653
Length
211 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTC
5' ss Score
7.04
3' ss Seq
CTCTCTGCCCTCGGGCGCAGGTT
3' ss Score
9.86
Exon sequences
Seq C1 exon
TGCGTTTTAAAAATTGTCTTTATTTACATTTTACAGAAAGTTGAGAAAGTGTTATTTATATGGGGGGTAGGGGTGCTGGAGATTATGAGACTAATAACAACCCTCTTAGCTCGCACCCTTTGGCACCACTACAGCTTCCAAACTCTGGGACTTTCTCGACTAGCTTCCCTTTGTTTAGCTGTGAAATGGAAGAAGCGGTCCGGGTGTGGCGGCTCATGCCTGTAACCTGAGCACTCTGGGAGGCGGAGGATCGCTTGAGTCCAGAAGTTCAAGACCAGCTTGGGCAACATAGGGTGACCCTCCACCCTCCCCCCGCCCCACCACATCGCTACAAAAAATTTTTAAAAATTAGCCGGGTGTGGTGGCGCAAGCCTGTAGTCTCAGCGGGAGCTGAGGGAGGAGAATCGCTTCAGCCCGGGAGGTCGAGGCTGTAGTGAGCCGAGATCGCGCTACTGCACTCCTGGGCGACAGAGCGAGACCCTGTCTCCAAAAAAAAAAAAAAAAGAAAAAAGAGGAAGTTGTATCCAATTCAGAAACGCGGTCCTTCGGGACCTGCTAGTTTTATACCCCGGAGGATCCTCCCCGGCGGGCTGGCACGGGAGGTGGAGAAAGAGGCTTGGGCGGCCCCGCTGTAGCCGCGTGTGGGAGGACGCACGGGCCTGCTTCAAAGCTTTGGGATAACAGCGCCTCCGGGGGATAATGAATGCGGAGCCTCCGTTTTCAGTCGACTTCAGATGTGTCTCCACTTTTTTCCGCTGTAGCCGCAAGGCAAGGAAACATTTCTCTTCCCGTACTGAGGAGGCTGAGGAGTGCACTGGGTGTTCTTTTCTCCTCTAACCCAGAACTGCGAGACAGAGGCTGAGTCCCTGTAAAGAACAGCTCCAGAAAAGCCAGGAGAGCGCAGGAGGGCATCCGGGAGGCCAGGAGGGGTTCGCTGGGGCCTCAACCGCACCCACATCGGTCCCACCTGCGAGGGGGCGGGACCTCGTGGCGCTGGACCAATCAGCACCCACCTGCGCTCACCTGGCCTCCTCCCGCTGGCTCCCGGGGGCTGCGGTGCTCAAAGGGGCAAGAGCTGAGCGGAACACCGGCCCGCCGTCGCGGCAGCTGCTTCACCCCTCTCTCTGCAGCCATGGGGCTCCCTCGTGGACCTCTCGCGTCTCTCCTCCTTCTCCAG
Seq A exon
GTACTCCACAGCCTCGCCGTGGCCCCGACCGGGACCGCTCCCTGGGGGGCGGGCGGGGTCCGCATGGGGCAGTGGCGTCGGGGAGAGCGCGGGGCTGCGCTCCCTGGGGCCAAGGGAGTCCCGGAAGGCCCGTGAGGACCCTGCGGTGTGGGGAGTGCAGGGCCGGGCACGCCTGGACCCAGCCTCCTTCACTCTCTGCCCTCGGGCGCAG
Seq C2 exon
GTTTGCTGGCTGCAGTGCGCGGCCTCCGAGCCGTGCCGGGCGGTCTTCAGGGAGGCTGAAGTGACCTTGGAGGCGGGAGGCGCGGAGCAGGAGCCCGGCCAGGCGCTGGGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000062038-CDH3:NM_001793:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.333
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF087586=Cadherin_pro=PU(38.9=71.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCAACCGCACCCACATC
R:
TCCAAGGTCACTTCAGCCTCC
Band lengths:
308-519
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)