HsaINT0031908 @ hg19
Intron Retention
Gene
ENSG00000039068 | CDH1
Description
cadherin 1, type 1, E-cadherin (epithelial) [Source:HGNC Symbol;Acc:1748]
Coordinates
chr16:68863557-68869444:+
Coord C1 exon
chr16:68863557-68863700
Coord A exon
chr16:68863701-68867192
Coord C2 exon
chr16:68867193-68869444
Length
3492 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGT
5' ss Score
9.82
3' ss Seq
TTTTGTCCCTTCTTCTTTAGAAT
3' ss Score
10.93
Exon sequences
Seq C1 exon
GACTTTGACTTGAGCCAGCTGCACAGGGGCCTGGACGCTCGGCCTGAAGTGACTCGTAACGACGTTGCACCAACCCTCATGAGTGTCCCCCGGTATCTTCCCCGCCCTGCCAATCCCGATGAAATTGGAAATTTTATTGATGAA
Seq A exon
GTAAGTAATCCACGTGGAAAGCCAAAGCATGGCTCATCTCTAAGCTCAGGAGGAGTTGTGTCAAAAATGAGAAAAAGAGTCTTTAGATTCTTTCCTTTACTATGTTTTCAGCTTGCCTGAGCCCTGGAGCCCTGTTTTCCTTTTTCTTTTTTTTTCTTTTTCTTTTTTTTTTTTTTTGAGACGAAGTTTCACTCTTGTTGCCCAGGCTGGAGTGCAATGGCGCAATCTTTGCTCACCACAACCTCTGCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGGCATGCACCACCACACTCAGCTAATTTTGTATTTTTAATAGAGGCAGGGTTTCTCCATGTTGGTCAGGCTGGTCTCTAACTCCTGACTCAGGTGATCCACCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGCACCTGGCAGCCTGTTTTTCTTAATCTGTGTCTCATCTGAATTTTGGATCTAATCGTGCTTCAAATTGCAAAGTCCATGTGGCAAAACCAACAATTGCCTGAAAGGATTTAGTAGATCTAGAAATGAAACTAGGAAGATTCTAAGTAAATTTCATTTTAGTTTCACTAATGGAATTTACTTCCCTTGCCTCCCACTGCTGGTTGGGATATAATGATAAATGTACATGACAAGCCTACCTGAGGATTAGAAAAATAGAATCTGTATTGTATATGTCAGAAATGCATTCAGCTCTAAATACAAGATGCTGAAACAGATGGGAGTAGATTTATCTTATACAAATAGAAAGTTGGGGTGAGCAGTCTAGGCCAGTGCATCAGGCTGTTCCATGTTTCTGCTCCATCATCTTAGCACGTAGACCCTTCTTCTCAGGCTTGTTGTCTCATGATCACAAGATGGCTGCCACACTTCCAGATCTTAAGTCTGTATTCCAGTCAGGAAAAAGTATGAAGAACAAAGCAGAGGGCAAAAGTCTTTCTTCTAGCAAACTGTCTTCTTATTCAACAAGGGAGTTGTCCAACCAGTTATTGGCCAGAACTATCAGAAGGTTGTGCCTGTCTGCAAGGGAGAATAACAAGGCATTAAATTAATTAGCTTAGGATAAGATGAGAAAGAACCCAGTAAAGAAATGGTCCAGCAGGATCTGTTTCCTTAAGTTATGTTCTCTAGTAACTTGCTTGGTTACTGGAATGATTTTCTGGGCTTGTCTGATGGTCCAGTGGCCCTCGGTGAGTCTTCATGGTGAGGTCTGTGTTTGCTTTAGCTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTTGCTCTGTCGCCCAGGCTGGAGTGCAGTGGTGCAATCTCAGCTCACTGCAAGCTCTACCTCCCAGGTTCACACCATTCTCCTGGCTCAGCCTCCCGAGTAGCTGTGCCTACAGGCACCTGCCATCAAGCCTGGCTTTTTTTTTTTTTTTTAATTTTATTTTTAGTAGAGACAGGGTTTCACCATGTTAACCAGATGGTCTCGATCTCCTGACCTCAGGTGATCTGCCTGCCTTGGCCTCCCAAAGTGTTGGGATTACAGGCGTGAGCCACCACGCCCGGACTGCTTTAGCTTTCTATGGGAGCTGTCACTGAGGACTGTGAGGCACTGCAGTGTTAGAAGTGATCAAGCCACATTCATTTTAGCCACTGGAAAAAACAAGAAACAGAAAGAAACCAGTTTAACCATGCCTTTTATTTATTTATTTATTTTTATTTTTATTTTCATTTTTTGAGACAGTTTCACTCTTGTCGCCCAGGCTGGAGTGCAGTGGCGTAATCTTGGCTCACTGCAACCTCTGCCTCCTAGATTCAAGCGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGGCACCACTACCACGCCCAGCTACTTTTTCTATTTTTAGTACAGATGGGGTTTCATCATATTGGCTAGTCTGGTCTCAAACTCCTGACCTCGGGTGATCTCCCTGCCTCGGCCTCCCAAAGTACTGGGATTATGGGTGTGAGCCACCGCTCCTGACTACAGACCCCTTTTAGATACATCTGGATTCAGGCCTTTCCTCCATTCATACTCATTTGCAAGTCATCACTTGTATTTGCAGTTTTTATTTAAACTATAAAAATAGTATGCTAAAAAAGAACAAGATCATGTCTTTTGAGGAAGCAAGATCATGGGTGGAGCTGGAGGCCATTATCCTTAGCAAACTAATGCAGGAACAGAAAACCAAATACCACGTGTTCTCACTCATATGTGGGAGCTGAATGATGAGAACTCATGGACACAAAGAAGAGAACAACAGACACTGGGGTTCGCTTAAGGGAGGAGAGAGAGAGGAGCAGAAAAGATAACTACTGGGTACTGGGCTAAATACCTGGGTGATGAAATAATCTGTACAACAAATCCCCATGACATGAGTTTACGATTTGTTACCTATATAACAAACCTTCACATGTACTCCCAAACCTAAAAGTTTTTTTTTTTTTAAGTATGCTTGCTATTTTAAAAATATAAATTATGGTGTGGGGGTACACACCTGTAATCCCAGCTACTCAGGAGGCTGAGGCCAGAGAATCGCTTGAACCCAGGAGGTGGAGGATGCAGTGAGCCGAGATCATGCCATTGCACTCTAGCCTTGGTGACAGAGCAAGACTCTGAGACTCCATCTCAAAATAAATAAATATACTTTATTTATTTCATAAAATGAAAATATATAAAGAAAAGGCCGGGTGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGTGGATCACCTGAGATCAGGAGTTAGAGACCAGCCTGGCCAACATGGTGAAACCCCGTTTTTACTAAAAATACAAAAATTAGCCGGGCATGGTGGCGCATGCCTGTAGACCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGCAGATGTTGCAGTGAGCCAAAATCACACCATTGCACTCCAGCCTGTGTGACAAGAGTGAAACCCTGTCTCTAAAAAAAAAGAAAAAGAAAAAAAATACAAGTCCTTCCTTAGTTCCCACACCCCCACTCCCCAGATTTAACTGTTAAGCATTTGGCATTTATCCTTCCAGGCCTTTCTGGGTGGAAATGCAGCCTGCATGCACCAGTATGCAAAGCTTCCAGCTCTGCCCATCCCAGCTGGTGGTGTGGCAGCCCCACTCTGATCTATGGGGACTCCATCCTGACTGGTTGGTGCTTGCATCTCTCCTGCCTACATATAACTCACCATTTCACTTTCTCTTTCCATCAACAACATATCCTGTGCTTCTGCATCCTTCCATGACAGTGTGTATAAATGTACGTTGTTGGTGTTCACTGCTCCGTGGTGTGCCACAAGTCTGGGTGCATTGTCGTACCTTACATATTGCTAGACTTCTTGCCCCAGATGACAGGTGTGCCCTTCCTTTCACTAAAAGATGCTTTTGTCCCTTCTTCTTTAG
Seq C2 exon
AATCTGAAAGCGGCTGATACTGACCCCACAGCCCCGCCTTATGATTCTCTGCTCGTGTTTGACTATGAAGGAAGCGGTTCCGAAGCTGCTAGTCTGAGCTCCCTGAACTCCTCAGAGTCAGACAAAGACCAGGACTATGACTACTTGAACGAATGGGGCAATCGCTTCAAGAAGCTGGCTGACATGTACGGAGGCGGCGAGGACGACTAGGGGACTCGAGAGAGGCGGGCCCCAGACCCATGTGCTGGGAAATGCAGAAATCACGTTGCTGGTGGTTTTTCAGCTCCCTTCCCTTGAGATGAGTTTCTGGGGAAAAAAAAGAGACTGGTTAGTGATGCAGTTAGTATAGCTTTATACTCTCTCCACTTTATAGCTCTAATAAGTTTGTGTTAGAAAAGTTTCGACTTATTTCTTAAAGCTTTTTTTTTTTTCCCATCACTCTTTACATGGTGGTGATGTCCAAAAGATACCCAAATTTTAATATTCCAGAAGAACAACTTTAGCATCAGAAGGTTCACCCAGCACCTTGCAGATTTTCTTAAGGAATTTTGTCTCACTTTTAAAAAGAAGGGGAGAAGTCAGCTACTCTAGTTCTGTTGTTTTGTGTATATAATTTTTTAAAAAAAATTTGTGTGCTTCTGCTCATTACTACACTGGTGTGTCCCTCTGCCTTTTTTTTTTTTTTAAGACAGGGTCTCATTCTATCGGCCAGGCTGGAGTGCAGTGGTGCAATCACAGCTCACTGCAGCCTTGTCCTCCCAGGCTCAAGCTATCCTTGCACCTCAGCCTCCCAAGTAGCTGGGACCACAGGCATGCACCACTACGCATGACTAATTTTTTAAATATTTGAGACGGGGTCTCCCTGTGTTACCCAGGCTGGTCTCAAACTCCTGGGCTCAAGTGATCCTCCCATCTTGGCCTCCCAGAGTATTGGGATTACAGACATGAGCCACTGCACCTGCCCAGCTCCCCAACTCCCTGCCATTTTTTAAGAGACAGTTTCGCTCCATCGCCCAGGCCTGGGATGCAGTGATGTGATCATAGCTCACTGTAACCTCAAACTCTGGGGCTCAAGCAGTTCTCCCACCAGCCTCCTTTTTATTTTTTTGTACAGATGGGGTCTTGCTATGTTGCCCAAGCTGGTCTTAAACTCCTGGCCTCAAGCAATCCTTCTGCCTTGGCCCCCCAAAGTGCTGGGATTGTGGGCATGAGCTGCTGTGCCCAGCCTCCATGTTTTAATATCAACTCTCACTCCTGAATTCAGTTGCTTTGCCCAAGATAGGAGTTCTCTGATGCAGAAATTATTGGGCTCTTTTAGGGTAAGAAGTTTGTGTCTTTGTCTGGCCACATCTTGACTAGGTATTGTCTACTCTGAAGACCTTTAATGGCTTCCCTCTTTCATCTCCTGAGTATGTAACTTGCAATGGGCAGCTATCCAGTGACTTGTTCTGAGTAAGTGTGTTCATTAATGTTTATTTAGCTCTGAAGCAAGAGTGATATACTCCAGGACTTAGAATAGTGCCTAAAGTGCTGCAGCCAAAGACAGAGCGGAACTATGAAAAGTGGGCTTGGAGATGGCAGGAGAGCTTGTCATTGAGCCTGGCAATTTAGCAAACTGATGCTGAGGATGATTGAGGTGGGTCTACCTCATCTCTGAAAATTCTGGAAGGAATGGAGGAGTCTCAACATGTGTTTCTGACACAAGATCCGTGGTTTGTACTCAAAGCCCAGAATCCCCAAGTGCCTGCTTTTGATGATGTCTACAGAAAATGCTGGCTGAGCTGAACACATTTGCCCAATTCCAGGTGTGCACAGAAAACCGAGAATATTCAAAATTCCAAATTTTTTTCTTAGGAGCAAGAAGAAAATGTGGCCCTAAAGGGGGTTAGTTGAGGGGTAGGGGGTAGTGAGGATCTTGATTTGGATCTCTTTTTATTTAAATGTGAATTTCAACTTTTGACAATCAAAGAAAAGACTTTTGTTGAAATAGCTTTACTGTTTCTCAAGTGTTTTGGAGAAAAAAATCAACCCTGCAATCACTTTTTGGAATTGTCTTGATTTTTCGGCAGTTCAAGCTATATCGAATATAGTTCTGTGTAGAGAATGTCACTGTAGTTTTGAGTGTATACATGTGTGGGTGCTGATAATTGTGTATTTTCTTTGGGGGTGGAAAAGGAAAACAATTCAAGCTGAGAAAAGTATTCTCAAAGATGCATTTTTATAAATTTTATTAAACAATTTTGTTAAACCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000039068-CDH1:NM_004360:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.438 A=NA C2=0.652
Domain overlap (PFAM):
C1:
PF0104912=Cadherin_C=FE(31.8=100)
A:
NA
C2:
PF0104912=Cadherin_C=PD(43.9=92.9)
Main Inclusion Isoform:
NA
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
- 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)