HsaINT0031904 @ hg19
Intron Retention
Gene
ENSG00000039068 | CDH1
Description
cadherin 1, type 1, E-cadherin (epithelial) [Source:HGNC Symbol;Acc:1748]
Coordinates
chr16:68853183-68856128:+
Coord C1 exon
chr16:68853183-68853328
Coord A exon
chr16:68853329-68855903
Coord C2 exon
chr16:68855904-68856128
Length
2575 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGG
5' ss Score
9.33
3' ss Seq
TTCTGTGTATTTTCTCTTAGGTT
3' ss Score
10.72
Exon sequences
Seq C1 exon
ATATCGGATTTGGAGAGACACTGCCAACTGGCTGGAGATTAATCCGGACACTGGTGCCATTTCCACTCGGGCTGAGCTGGACAGGGAGGATTTTGAGCACGTGAAGAACAGCACGTACACAGCCCTAATCATAGCTACAGACAATG
Seq A exon
GTAAGGGGGCCTCATCTGAGCCTTTGCTGCCTCGACCTCCTAGCTAGTTCAGTTCCTTGCCCCTCCCTTCTTTTGGAGGGAAGAGTTCATTCTTTTTCTTTTATCCTTTTTGTTTGCTGGATTGATTTGTATAAATGTATGGAGTACAAGGGTAATTTTGTTACATGCATAGATGTGTAGTGGTAAAGTCAGGGCTTTTAGGGTATCCGTCACCCAAATAACATGCATTGTACCCATTAAGTAATTGTTCATCATCTACCCCCTCCCACCCCTTGGACCCTTCCCAGCTGCCATTGTCTATCATTCCACAATCTACATCCATGTGTACACATTATCGAACTCCGACTTCTAAGTGAGAACATGCAGTATTTCTCCTTATATGTCTGATTCGTTTCACTTGAGACAATGGCCTCCAGTTTCATCCATGTTGCTGCAAAAGATTTCTCTTTTATTCTTAAACAAAGGCATTCTTATTATCAAAAATTCAAGTGGGCTGGGCACGGTGACTCACACCTGTAATCCCAGCACTTAGAGAGGCTGAGGTGGGAGGATCACTTGAGCCCAGGAGTTCAAGACCAGCCTGGGTAACATGGCAAAACCCTGTCTCTACAAAAAGTACATAAATTAGCTGAGTGTGTTGGTGAGCACCTGTAGGCCCAGCTACTCAGAAGGCTGAAGTGGTAGGATTGCTTGAGTCTGAAAGGTGGAGGCTGCAGTGAGCCAAGATTGCGCCACTGCTCTCCATCCTGGGCAACAGAGCAAGACTCTGTCTCCAAAAAAAAAATTGTTTTTTCAAGTAATTTTGGTCAAACAGAACTTACTTTTCACTACTCACTCTTTATTCCTTCCCTAAGGGAACCAGGTAATGATGGTTTACAATCCATTTCCAAAGCTTAATACTTGTGTGACCTTGGATTTGCTGTTTAATTTTTTTTTTTTTTTTGAGACAGAGTCTTGCTCTGTCACCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTGCAGCTTCCGCCTCCCAGGTTCAAGCAATTGTCCTACCTCAGCCTCCCAAGTAGCTGGGATTACAGGTGTGCACCACCACGCCCAGCTAATTTTTTGTATTTTTAGTAGAAACGGGGTTTCACCATATTGGCCAAGCTGGTCTTGAACTCCTGACCTTGTGATCTGCCCACCTTGGCCTCCCAGAGTGCTGGGATTACAGGTGTGAGCCACCGTGCCTGGCCTGCTGTTTAATTTTTATGTCCCTCAATTCCTTTACCTGAAAAATGTTAATACCCATGTGGGTGAAATTAGTTAGGTGTTAAATCAGTTAGGTGTGGGTCCTTCCAGACTGCTTCTGTGTATTTAAATACATTTATAGGCTGGGTGCTAGGGTCACACCTGTAATCCCAACACTTTGGGGGTCTGAGGTGGGAGATGGCTTGAGGCCAGGAGTTCAAGACTAGCCTGGGCAACATACTGCCCATAATCTCAAAATGCTGGGATTACAGGCATGAGTTATCATGCTTGGCCTCCTTGAGTTAATTTTAAATGACGTGTGCTCATTGTTAAAAAATAAAATTTACATGAGAAAAAAGTTTTAAAAATTTACAGTCATGCCATCTAGACATATCTATTTATAGGTTTGAGATGGATTCTTCTGTTGTTTTGTATCCGTATCGTATACTAATATTGATGATAGTTCCCTGGGTACCAATTTTTCCTACTACCATATGCTCCGTGTTGTGTCAAGATATAAAAGAAATGCAAACAGAAGTGTGGATGGGCTGGGCGCAGTGGCTCACGCCTATAATCCCAACACTTTCAGAGGCTAAGATGCGAGGATCACTTGAGCTCAAGAGTTCAAGACCAGCCTGAGCAACATGATAAGACCCCCTCTCTACAAAAAAAATTTAAAAACTAGCCAAGCATGGTGGCATGCGCCTGTAGTCTCAGCTACTAGGGAGGCAGAGGTGGGAGATTAAGCCCAGGAGGTAGAGGCTGCAGTGAACTGTGTTCATGCCACTGCATTCCCGCCTGGGTGACAGAGTGAGACTCTGCCTCAAAAAAAAAAAAAAAAGCGTATGTGAACTCCCCAATCTATTTTGAAAACCAATTTGCAGAGACTTCAAAAGACCCAACTCATCCCCTTTGATTTTAAGCTTCTAGTCAGGCTTAAAATTAAAATAAATAAAAAGACTCAATGCTTTGTTAATGACCTCAAATGGCAGGAAAGTGCAGAAAAAGGAGAACTAGGGAAACAACAGGCAGGCAATAGGACTTCTTGGAGTAGTTAAAATTCAGTGAATGAATAACGATATGTGAAGAAGGAGGAGTGTGTTCTTGGTGTGAGGAATAACTTGAATAATTGTTATCAAGGTGGGAATAAGTTGTCTGTGTAAAACGGCCAGAGACCTGCCCACCTGGGAGTGGAGGTCCTTTGGGATTGGTGGGACAGGAGGTTCTGCGGGTGGAGTGGGGCCTGGTGAGGGACCACTGAAGAGCCAGGACAAGATCTAGACTTGGTCTGGTGGAAGGCAATGGGGATTCATTACTGTTGCCAAGCTGCCACATTTTCTGTGTATTTTCTCTTAG
Seq C2 exon
GTTCTCCAGTTGCTACTGGAACAGGGACACTTCTGCTGATCCTGTCTGATGTGAATGACAACGCCCCCATACCAGAACCTCGAACTATATTCTTCTGTGAGAGGAATCCAAAGCCTCAGGTCATAAACATCATTGATGCAGACCTTCCTCCCAATACATCTCCCTTCACAGCAGAACTAACACACGGGGCGAGTGCCAACTGGACCATTCAGTACAACGACCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000039068-CDH1:NM_004360:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.180 A=NA C2=0.092
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=FE(51.6=100)
A:
NA
C2:
PF0002812=Cadherin=PD(14.7=18.4),PF0002812=Cadherin=PU(53.9=63.2)
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:
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)