HsaINT0032174 @ hg19
Intron Retention
Gene
ENSG00000062038 | CDH3
Description
cadherin 3, type 1, P-cadherin (placental) [Source:HGNC Symbol;Acc:1762]
Coordinates
chr16:68729680-68732957:+
Coord C1 exon
chr16:68729680-68729826
Coord A exon
chr16:68729827-68732093
Coord C2 exon
chr16:68732094-68732957
Length
2267 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
CCTGTTCTCTGTTGCCGCAGAAC
3' ss Score
10.1
Exon sequences
Seq C1 exon
GACTATGACATCACCCAGCTCCACCGAGGTCTGGAGGCCAGGCCGGAGGTGGTTCTCCGCAATGACGTGGCACCAACCATCATCCCGACACCCATGTACCGTCCTCGGCCAGCCAACCCAGATGAAATCGGCAACTTTATAATTGAG
Seq A exon
GTGAGGCGTGGCAGGCCAGTCGAGGGCCACCCTTTATTCAAGCCCAGCACCAGCCACACAGGAGAACAAGCATGGGCCTGGAGTCTTGGGTCTGGGTTCAAATTCTGACTCCACCACCAACCAGCTTTTGACCTCTGGCTTATTTGAGTAACTTCTGGGGTTTGTTTCTTCCTCCATAGAACTCACTTGCAGAGTGGTTAAAAATGATTAGGAGGGGCTGGGCACGGTGCCTCACGCCTGTAATCTGAGCACTTTGGGAGGCTGAGACGGGTGAATCATGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGCGAAACCCCATCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGGCGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTGAGCACAAGAATCGCTTGAACCAAGGAGGCAGAGGTTGCAGTGAGCCGACATCACGCCACTGCACTCCAGCCTGGGTGACAGAGCAAGACTCCATCTCAACAACAACAACAAAAATGATTAGGAGGCTGGGCACAGTGCCTCACGCCTGTAATCTCAGAACTTTCAGAGGCCAAGGTGGGCAGATCACTTGACGTCAGGAGTTTGAGATCAGCCTGGCCAACATGGTGGGAGGTGGAGGTTGCAGTGAGCCAAGATCGCACCTGGGTGCAACTTATGGCTGTAGTGAATGCCGAGAATGAAGTACTCAGACAATTCTAGCTGAGCGGGGCGGGGAGCAGTTCCTTTGAGAGAGCGTCACTCTAAGATCTGTCTGCCAGGTATTTATTGAGAGAGCTTGTTTAAACTACAATTTAGACAAACAAGAGACATCCACCAGGTGGCTCTTGGCGGTCGGGTATGAGGCACATATGGCCTTGTAAAAAACACTCAAACCACATTTTTAGGAGGCTGTGTTCAGCGCTCCTTATCACACATACTACTCCCTGTCCTGTTTTCAAGGTCCAGGAGATCTAGTCTTGTGTACAAACAACATGCACACAGCGCCTCAATATTTTTCCATGCCTCGACCTCACATGCCTCTTACATAGGCTTGAATGTCTTGTCGTGCGCCCCCCACACCTGGGCAACAAAGGGAGACTCCATCTCAAAAAAAAAAAAAAGGCCGGGCACAGTGGCTCATGCCTGTAATCCCACCAGCACTTTGGGAGGCTGAGGCGGGCAGATCACAAGGTCAAGAGATTGAGACTATCCTGGCCAACATGGTAAAACCCTGTCTCTACTAAAAATACAAAAAATTAGCTGGGCGTCCTGGTGGGCGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCCAGGAGGTGGAGGTTGCAGTGAGCCGAGATCACATCATTGCACTCCAGCCTGGGCAACAAAGGGAGATTCCATCTTTAAAAAAAAAAAAATTAGGAATGATTTATTCATTTATTCAACACATATAGCAGTTGAATACTCTGGAGCCAGACTACCTGGGTTTGGATTATAGATCCCAGGTGATTGCACCTGGGGGGCAAAGTTTGGAGCCTCTGCTGTAGAAGACTTCAAGGATTGAACGAGCAGGCAGCTAGGACAGTGCCAGCACAGTGGTTCCCGACCCTGCCTGCGTGTTGGAATCACCTGGGCACCTTCAGAAACCACTGATGCCTCAGCTCACCTCCAAAGATTGTGATATAATTGAACTGGGTGTGGCCTGGGCTTCAGAATTTATAAAAGATTCTCCAGATAATTTAAGTTTCGGAACTACTGACCTAGCATGTAGCGCTTATTAGATAATGATAGCTATTGTTGCGAGGTGCTATTCTAATAACTGCTTTACAGGTATTTACTCATTTACTCATTCATCTGTTCCTTTAAAACTATACGGAGGCACATGTCCTCAGTACCTCCCGAGGCTGTGTCACAGGCATGCATCCTTTAAAAAAGGAAGAAAAAAACTATTGTCATTTTACAGACAAGGAAACAGGCATAGAGTGGTTAAGGGACTCGCCCAAGGCCACAAAGCTAGTGTGTGGTGTGAGTTCTGGCCCGGGCTGTCTGATTTCAGTCCTTGCCCTTACCCCCTGGCCTGTGTTGCACTGAGCACTTGCTGTCTGCTGGTCCCTGAGTGAATGAATTCTGCATGAATAACGCATTCTTTCATTTCTACCTCCAAAACCTTTAGGGGAGGGGAGAGAGGGGCTCACAGAGAGGAAATGGAGGCTTGCAGCTGGCAAGAGGCAGGACCCGCCGCTCCTAACTACCTGTTCTCTGTTGCCGCAG
Seq C2 exon
AACCTGAAGGCGGCTAACACAGACCCCACAGCCCCGCCCTACGACACCCTCTTGGTGTTCGACTATGAGGGCAGCGGCTCCGACGCCGCGTCCCTGAGCTCCCTCACCTCCTCCGCCTCCGACCAAGACCAAGATTACGATTATCTGAACGAGTGGGGCAGCCGCTTCAAGAAGCTGGCAGACATGTACGGTGGCGGGGAGGACGACTAGGCGGCCTGCCTGCAGGGCTGGGGACCAAACGTCAGGCCACAGAGCATCTCCAAGGGGTCTCAGTTCCCCCTTCAGCTGAGGACTTCGGAGCTTGTCAGGAAGTGGCCGTAGCAACTTGGCGGAGACAGGCTATGAGTCTGACGTTAGAGTGGTGGCTTCCTTAGCCTTTCAGGATGGAGGAATGTGGGCAGTTTGACTTCAGCACTGAAAACCTCTCCACCTGGGCCAGGGTTGCCTCAGAGGCCAAGTTTCCAGAAGCCTCTTACCTGCCGTAAAATGCTCAACCCTGTGTCCTGGGCCTGGGCCTGCTGTGACTGACCTACAGTGGACTTTCTCTCTGGAATGGAACCTTCTTAGGCCTCCTGGTGCAACTTAATTTTTTTTTTTAATGCTATCTTCAAAACGTTAGAGAAAGTTCTTCAAAAGTGCAGCCCAGAGCTGCTGGGCCCACTGGCCGTCCTGCATTTCTGGTTTCCAGACCCCAATGCCTCCCATTCGGATGGATCTCTGCGTTTTTATACTGAGTGTGCCTAGGTTGCCCCTTATTTTTTATTTTCCCTGTTGCGTTGCTATAGATGAAGGGTGAGGACAATCGTGTATATGTACTAGAACTTTTTTATTAAAGAAACTTTTCCCAGAGGTGCCTGGGGAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000062038-CDH3:NM_001793:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.327 A=NA C2=0.377
Domain overlap (PFAM):
C1:
PF0104912=Cadherin_C=PD(62.0=66.3)
A:
NA
C2:
PF0104912=Cadherin_C=PD(43.3=92.9)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
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]
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)