HsaINT0031905 @ hg19
Intron Retention
Gene
ENSG00000039068 | CDH1
Description
cadherin 1, type 1, E-cadherin (epithelial) [Source:HGNC Symbol;Acc:1748]
Coordinates
chr16:68855904-68857529:+
Coord C1 exon
chr16:68855904-68856128
Coord A exon
chr16:68856129-68857301
Coord C2 exon
chr16:68857302-68857529
Length
1173 bp
Sequences
Splice sites
5' ss Seq
CAAGTGGGT
5' ss Score
4.82
3' ss Seq
CTTTTTATTGCTTTCTCCAGCCC
3' ss Score
8.25
Exon sequences
Seq C1 exon
GTTCTCCAGTTGCTACTGGAACAGGGACACTTCTGCTGATCCTGTCTGATGTGAATGACAACGCCCCCATACCAGAACCTCGAACTATATTCTTCTGTGAGAGGAATCCAAAGCCTCAGGTCATAAACATCATTGATGCAGACCTTCCTCCCAATACATCTCCCTTCACAGCAGAACTAACACACGGGGCGAGTGCCAACTGGACCATTCAGTACAACGACCCAA
Seq A exon
GTGGGTACCTGAGTTTTATTTTGGCAACTTTGCTCCAACTGCCATGCTTCCCTTCCCCCAGATCCCCACCTTTCAATTTCCCTTCTCAACTTCTAGATGTCACCCCTTCCATTGATACTTGCTTCCTTGTCCCTTCTGTCTTTGAGGCCTTGCTCCAAAGGTCTTTTTCCTTTCCTGGTATCTAACTTTGTAGCATGCTACCCAGTAATCTAAAACCCAAGCAGGGCTCCCTCTCCCAGCCTCTAGCCACCCTCCACTCCCCTCTCCACTTGCAACCAGGACCATCTTCTCTGCTACCTCCTGCTCCTGGGACCAAACAACACCATTTTTGTGGTTAGCTCCTTCTTGCCAACCAATCGTGAGCTCCCAGATTCATCAGAACTATTCTACCGAGGTGGAGGCAGCTGTCAACTGCCTGGTCAATTTGCATATATGGGCTTCCTACACCTACTTCTCTCTGGGCTTCTATTTCCACCATGACGATGTGGATCTGGAAGGTGTGCACCACTTCTTCCACAAATTGGCCAAGGAGAAGCACAAGGGCGCTGAGTGTCCCTTGAAAATGCAAAACCAGTGTGGCGGCCGCACTGTCTTCCCGGACATCCAGAAGCCATGTAAAGATGAATGGGGTAAAACCCTGGGTGCGATGGAAGTCACTCTGGCCCTGGAGAAGAACCTGAACTGGACCCTTTTGGATCTTCATGCCTTGGGTTCCACCTGCACAGACCCCCATATCTGTGACTTCCTGGAGAGCCACTTCCTAGATGAAAAAGTAAAACTCATCAAGAAGATAGGTGACCACCTGACCAACCTTCACAGGCCAGCCGGCCTCCAGGCCGGGCTGGGCAAAAAGGTTCACCCTCAGGCACACGGGAGCCTACCGAACCCAGCGACATCTGAAGAGCCCCGCTCTGCCTAAGCCTCTCCCTCCAGCCACTAGGCAGCTTTTTTAAACCAACTCTAGAGCCCTCTCCCAAGCCTTAGACCAAATGGAAATAAAGCTTTTTACAGCAAAAAAAAAAAAAAAAAAGTACATACCTAAATAAAACCCAAGCAGCTCTGCTCTCTTCACTCGGCTTGCGGGTGTCTTTAGTTCACTAGCAATTTTATTCTGGAATGAGCTTTTTATTTTCCTCCCCTGGTCTCATCATTTCTTTTTATTGCTTTCTCCAG
Seq C2 exon
CCCAAGAATCTATCATTTTGAAGCCAAAGATGGCCTTAGAGGTGGGTGACTACAAAATCAATCTCAAGCTCATGGATAACCAGAATAAAGACCAAGTGACCACCTTAGAGGTCAGCGTGTGTGACTGTGAAGGGGCCGCTGGCGTCTGTAGGAAGGCACAGCCTGTCGAAGCAGGATTGCAAATTCCTGCCATTCTGGGGATTCTTGGAGGAATTCTTGCTTTGCTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000039068-CDH1:NM_004360:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.092 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(14.7=18.4),PF0002812=Cadherin=PU(53.9=63.2)
A:
NA
C2:
PF0002812=Cadherin=PD(44.9=51.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGATGTGAATGACAACGCCCC
R:
CAATCCTGCTTCGACAGGCTG
Band lengths:
358-1531
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)