DreINT0043962 @ danRer10
Intron Retention
Gene
ENSDARG00000102750 | cdh1
Description
cadherin 1, type 1, E-cadherin (epithelial) [Source:ZFIN;Acc:ZDB-GENE-010606-1]
Coordinates
chr7:52830130-52830664:-
Coord C1 exon
chr7:52830446-52830664
Coord A exon
chr7:52830355-52830445
Coord C2 exon
chr7:52830130-52830354
Length
91 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
ATTACATTTGCCAATTATAGAAA
3' ss Score
5.31
Exon sequences
Seq C1 exon
TTGAGTCTCCAGCAACTGGCACAGGAACACTGGTAATTGAACTGCAGGATGTAAATGACAATGCTCCTGTTATTAATGAAAGGACCATAAAATTGTGCAATCGTGAATCAGCCCCAGTGCTTCTCTCTATAACGGACAAAGATTTACCTCCTTTTGCTGGTCCCTTCAAAGTTGAGCCCCAAGGTGATACCAGTAAAAATTGGTCTGTTTTTTTCAATG
Seq A exon
GTGAGTAAATGTTTGTTTTATTTTATATATATATATATAGTTCATCTGACTTTGAGTGGACATCTCTAACTATTACATTTGCCAATTATAG
Seq C2 exon
AAACTGGTCATTTTCTGAATATCAAGCCTCAATCTCAGTTGGAACAGGGTGAATACAAGGTGGTCCTGAGAGTTGCTGATCGGGAGGGTGAATCTCAGGAGAATATTATTCAAGCAAGTGTGTGTGACTGCAAAGGAGAGGCATTCCAATGTACTGATAAACAAGTAGCAGGGATTCCACTGTTTGGAGTTCTTGGTGTCCTGGGAGGAATCTTACTTCTGCTAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000102750:ENSDART00000167882:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.135 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(15.8=20.3),PF0002812=Cadherin=PU(52.3=62.2)
A:
NA
C2:
PF0002812=Cadherin=PD(46.6=53.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCCTTTTGCTGGTCCCTTC
R:
CCTGAGATTCACCCTCCCGAT
Band lengths:
172-263
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]