HsaINT0032171 @ hg19
Intron Retention
Gene
ENSG00000062038 | CDH3
Description
cadherin 3, type 1, P-cadherin (placental) [Source:HGNC Symbol;Acc:1762]
Coordinates
chr16:68721415-68725829:+
Coord C1 exon
chr16:68721415-68721639
Coord A exon
chr16:68721640-68725622
Coord C2 exon
chr16:68725623-68725829
Length
3983 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCT
5' ss Score
8.49
3' ss Seq
CAATGATCTGTTCACTCCAGGTG
3' ss Score
7.6
Exon sequences
Seq C1 exon
GAAGCCCTCCCACCACTGGCACGGGAACCCTTCTGCTAACACTGATTGATGTCAATGACCATGGCCCAGTCCCTGAGCCCCGTCAGATCACCATCTGCAACCAAAGCCCTGTGCGCCAGGTGCTGAACATCACGGACAAGGACCTGTCTCCCCACACCTCCCCTTTCCAGGCCCAGCTCACAGATGACTCAGACATCTACTGGACGGCAGAGGTCAACGAGGAAG
Seq A exon
GTACCTGAGTGAGTGGTGGTAGCGGGTGGGGTGCCAGCCCCACTGGTGGGCATCTGCCCCACACCAGGATTCTGCACACGTTCCTATCCTAGCATCTTGTGGGCCATGGGGACAATGATCTCCTCTAGAACCTCAATCAGATGCTATTTATTAACCTGGTGGAGGTCTTTGAAATTCCACAGGACCCCTAAAAGACCATTCTAGCCCAACCGCCTTCCTGTGTAGATGGAAAAACTGAGGCCTCGAGGAATCGAACCTATGTAGAGCATGTGAAGTGGACCTGGCACAGAGCATGCTCAGTGAGTGTTGGCTACGATCACTGTGCTGGGTCCTGACTCTCGCTATGTGACATGGGCCAAGTCACTCCCTCCCTCTCGAGGCCTCAGTTTTTCCATCTACACAGGAAGGCGGTTGGGCTAGAATGGTCTTTTAGGGGTCCTGTGGAATTCCAAAGACCTCCACCAGGTTAATAAATAGCATCTGATTGAGGTTCTAGAGGAGACCGTTGCCCCCGTGGCCCACAAGATGCCCACCACACCCGGCTGCGTTATGGCTTTAAAAATAATGTCATGGCCACACGCAGTGGCTTACACCTGTAATCCCAGCACTTTGGGAGCCTGAGGCGGGCGGGTCACCAGGTCAGGAGTTCGAGACCAGCCTGGCCAATATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGGCATGTGCCCGTAGTCCCAGTTACTCAGGAGGCTGAGACAGAAGAATCGCTTGAAGCCGGGAGGCGGAAGTTGCAGTGAGCCGTGATTGTGCCACTGTACTCCAGCCTGGACAACAGAGTGAGACTGTCTCAAATAAAATAAAATTAAAATGTCACTAGGGTTTTTTGTTTTTGTTTTTGTTTTTGTTTTGAGACGGAGTCTCACTCTGTCTCCCAGACTGGAGTGCAGTGGCACAATCTCAGCTCACTGCAACCTCCGCTTCCCGGGTTCAAGCAATTATCCCTGCCTGAGTAGCTGAGATTACAGATACCTGTCACCATGCCCATCTAATTTTTGTATTTTTTAGTAAAGGCATGGTTTTGCCATGTTGGCCAGGCTGGTCTTGAACTCCTGACTTCAGGTGATCCTCTCGCCTTGGCCTTCCAAAGTGCTGAGATTACAAGCATGAGCCACCACACCTGGCCTATCAGGATTTTAATCTAGGCAGTCTCACTCACCATGGTGTGGAAAATAAAAAGCATAAGCATTATGGCCAAAACCCAGTGTTATTAATACCTGTAACAGTATTGATCAGTATTGATAACCTGGTTCTTGGCTTTAATTTCATTTTTCTGTTTGCCCTTGTTCTGTTGTCAGGGAAATTAATCTAGACTCTACTCCATGTGACCTCAGGCTAGTTACCTAACTCCCTAAGCCTCAATTTCTGCATTTGTAAAATGAGGATAACAGCAGTTCCCACCTCTTAAAGCAATGGTGAGGATCAGGGTAGGGCCTGGCACTTAGTAAGTGCCCATTTAGCCGGGCAAGGTGGCTCATGCCTGTAATCCCAGCACTTTAGGAGGCTGAGGTGGGCGGATCACGAGGTCAAGAGGTCAAGACTGTCCTGGCCAACATGGTGAAACCCTGTCTCTACTAAAAATATAAAAAATAATTAGCCAGGCGTGGTAGCACATGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGTGGAAGTTGCAGTGAGCCAAGATCGCGCCACTGCACTCCAGCCTGGGTGACAGAGCGAGACTCTGTCTCAGAAAAATTAAAAAAAAAAAAGAAAGAAAGAAAAAGTGCCCATTTAGTCACCACTGCCATCGTCATCAACAACTGAGAAATCAGCCTTATAGGATGGCAGAGATGTTTTAGTGACATATACCCCATGTTGGCCACTCCACATGGTCGACTAGTTGTTCAGACTGGAGAGCTGTCTCTGCCTCCTGGCACTAAATGGGGACAGAGTGGATTCTGCCTTCTGGCCCTTTGACTAAGAGGAGCCCAGCGAGAGTGCAGAGCATTTTAACTTGAAATCTGTGCTGAGATAGGCTGACAACCCGGGGAGGGGGTGGGGGTAGAAACGTGGGGGTTGTTTTTGATTGCCCCAGTGATTGGGGGCACTACGGGCATTTAGTGGTAGAAACCCGCAATGCTGTGGCAAATCCTGCATGATGAAAAAACTTCCACACAGGCTAACAGCTCCCTTCTTGAGAAAGTTGAGTCTAAACCAAAGGCCTTTCTTTAAAGAGGCCACTGATATTATGTTCGTCACCCACACACATAGCCCCTTCTCCACTCTGGGATTGCCACGCAGTCTCCCCCGAGTGGTGCCCAGTGTGCAGGCTGGGCTGGGCCTGGCTTCTGCTCTGTGGTTAGCCTGCCACCCCCTGGGCCTTGGAAGGCCAGTTAGCCCAATACCTGCTGCAGCCTCATTTCTGACATTCCTGCATTTGTGTGATCACTAATGCTGTGATAACACAGGTTAGCATCTGATCGGATCTGCTCAACATTAGCACTTACATAACCAAGTCATGTGCGTTTAGTTTTATTAATAATTGAATGCGGCCTGGCATTGTGGCTCAGGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGGCAGATCACCTGAGGTCAGGAGCTTGAGACCAGCCTGACACAAAATCCACCTCTGCTAAAAATACAAAAACTAGCTGGGTGTAGTGGCGCAAACCTGTAGTCCCAGCTACTCCAGAGGCCAAGGCAGGAGAATCGCTTGAGCCCATGAGGCAGAGGTTGCAGTGAGCTGAGATCGCGCCACTGTACTCCAGCCTGAGTGATAGAGCAAGACTCTGTCTAAAAAAAAAATTGAAGGCCGGGCACCGTGGCTCACGCCTGTAATCCCAGCACTCTGGGAGGCCGAGGAAGGTGGATCACGAGGTCAGGAGTTTGAGACCAGCCTGGTCAAGATGGTGAAAGCCTGTCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGGCGGGTGCCTGTAATCTCAGCTACTCAGGAGGCTGAGGCAGGAGAATAGCTTGAACGTGGGAGGCGGAGGTTGCAGTGAGCTGAGATCACGCCACTGCTCTCTAGTCTGGGTGACAGAGCAAGACTTAGTCTCAAAAAAATTGAATGCTCAGTTGGAAATATGGGTGTTTCATATAAGATTGGGCTAGCTATCAGCTGCTCTGTCTATGGAGTAGCCATTCTTTATTCCTTTACTTTCTTTTTTTTTTTTTTTGAGACAGTCCTGCTCTGTCGCCAGGCTGGAGTGCAGTGGCATGATCTCAGTTCACTGCAACCTCCACCTCCCAGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCACGTGCCATCACGCCTGGCTAATTTTTGTATTTTTAGTAGAGACGGGTTTTCACCATGTTGGCCAGGATGGTCTCGATCTCTTGACCTCGTGATCTGCCCACTTCGGCCTCTCAAAGTGCCGGGATTGCAGGCATAAGCCACTGCGCCCAGCCCTCCTTTACTTTCTTAATAAAGTTGCTTTTACTTTAAAAAAAAAATGGGTTAGCTATCTTTTAGGAAGAATATTCTTTTTGAAGCAAAAAAACAGTGTAGCAGCCAATGATGCAAAGAAGTTATTGGTCCTGCATGACATGGCTTTTAAAACTTCATGTTATAAAAATACTGTGATTATTGATTTTTTTAAAAGTAAAATGACAAATTAATTTTTCTATCCCAATAATCCTTTTCATTATGGTGAATTTTGCTTTAGCCAAAGATCAGCTTTTACTGCTATTTTCCAAAGTGTGCTTGTGGAGTATTTCTCTGCATTGCCCACATGTGGAAGCCGTATTCTCAAACTTTCTTCATGGTGTACTCAGATCCCCGCACTGATGGTTCCCACAGCTAATCAATGATCTGTTCACTCCAG
Seq C2 exon
GTGACACAGTGGTCTTGTCCCTGAAGAAGTTCCTGAAGCAGGATACATATGACGTGCACCTTTCTCTGTCTGACCATGGCAACAAAGAGCAGCTGACGGTGATCAGGGCCACTGTGTGCGACTGCCATGGCCATGTCGAAACCTGCCCTGGACCCTGGAAGGGAGGTTTCATCCTCCCTGTGCTGGGGGCTGTCCTGGCTCTGCTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000062038-CDH3:NM_001793:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.289 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(15.8=19.7),PF0002812=Cadherin=PU(54.5=63.2)
A:
NA
C2:
PF0002812=Cadherin=PD(44.3=55.7)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
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
- 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)