HsaINT0032186 @ hg38
Intron Retention
Gene
ENSG00000179242 | CDH4
Description
cadherin 4 [Source:HGNC Symbol;Acc:HGNC:1763]
Coordinates
chr20:61928190-61929842:+
Coord C1 exon
chr20:61928190-61928423
Coord A exon
chr20:61928424-61929608
Coord C2 exon
chr20:61929609-61929842
Length
1185 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGC
5' ss Score
9.44
3' ss Seq
TTACTGTTGCTTTGCACCAGGTG
3' ss Score
9.55
Exon sequences
Seq C1 exon
GGATACCCCCGGCCAGCGGCACCGGGACCCTCCAGATCTATCTCATTGACATCAACGACAACGCCCCTGAGCTGCTGCCCAAGGAGGCGCAGATCTGCGAGAAGCCCAACCTGAACGCCATCAACATCACGGCGGCCGACGCTGACGTCGACCCCAACATCGGCCCCTACGTCTTCGAGCTGCCCTTTGTCCCGGCGGCCGTGCGGAAGAACTGGACCATCACCCGCCTGAACG
Seq A exon
GTGAGCCCGCCTTAGGCCACGGGGAGGGTCAGACTAGCCTGGGGTGCAGGCCCCTGGGAGACCCAGCTGGCCTTGGAAGAGTGGGCACCAGAGGTGGGTGACAGTCCTCCAACAGGACTGTCCCACCAAGGCTGGGGACACTGGCCACGCTTCAGCTGCTCAGCCTCCTTCACCTGGCCTTGAGGAGGCCACCAAGTCATTCCCAATTTCTTGCTGCTTTAATGAGGCCAGCCGTGAACATCCTTGCAGCTCTGCCCATGTACATCCATGACAACTTCCTGTGCCGGTTGTCAGTTGACTGGACCCTGACTGATATGTTTCCTTAGAATACTTCCCTGGATGCAGATCTGTGGTATAAAAGGATATCAAAATTCTCAAGTTTTGGCAGTACTGTGAAAATGTGCTCTAAACATGTCTACTTCCATCGGGAGAGTGCCTGTTTGTTTCCTCAAACCCCACCAACACTGAACATTATTGTTTTAAAATAATATTTTATTCTGCCACCTTTAGGCCAAAGTCATTATTTCCATTTGTATATCCTGATTACCAGTGGAAATTTTTTATATATATTTATTGGCCATTTTTGTTTCTTCTGTGAATTGTCTGTTCAATGACTTTGCCTATGTTTTCTTTGGGGAGTTTCTTTTTATTGATTTGGTAAAACTCTTTATATATTCAGGAAATTATTTCTTCATCCTACATGTTGCAATTGCTTTTTGGTTGTGTCTCCAATGTCTTTTTTTTTTTGAGACTGTTGCCCAGGCAGAAGTGCAGTGGCACAATCTCAGCTCTGCAACTCCACCTCCCAGGTTCAAGCAATTCTCCCACCTCAGGCTCCCAAGTAGCTGAGATCACAGGCTTGCACCACACGCCCGGCTAATTTTTGTATTTTTTACTAGAGACAGGGTTTTGCCATGTTGGCCAGGCTGGTCGTGAACTCCTGACTTCAAGTGATCTGCCCACCTCAGCCTCCCAAAGTGCTGGGATTACAAGCGTGAGCCACCACACCCAACCTCCAATGTCTTTTAACTTAATGATGTAGCACAGGTGTATGTATGTATGTGTGGTAACCAGGCAGCCATTTCAGATTTCCATGCCATCGGACTTTTAGTCTTTTCCTTTGGACGTCTTGCTTGGAAGCGAGGGCCGGGCTCTGGTTGAATGTTTACTGTTGCTTTGCACCAG
Seq C2 exon
GTGACTATGCCCAACTCAGCTTGCGCATCCTGTACCTGGAGGCCGGGATGTATGACGTCCCCATCATCGTCACAGACTCTGGAAACCCTCCCCTGTCCAACACGTCCATCATCAAAGTCAAGGTGTGCCCATGTGATGACAACGGGGACTGCACCACCATTGGCGCAGTGGCAGCGGCTGGTCTGGGCACCGGTGCCATCGTGGCCATCCTCATCTGCATCCTCATCCTGCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000179242:ENST00000614565:12
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
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGGGACCCTCCAGATCTATC
R:
CACATGGGCACACCTTGACTT
Band lengths:
348-1533
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