DreINT0043963 @ danRer10
Intron Retention
Gene
ENSDARG00000102750 | cdh1
Description
cadherin 1, type 1, E-cadherin (epithelial) [Source:ZFIN;Acc:ZDB-GENE-010606-1]
Coordinates
chr7:52829476-52830354:-
Coord C1 exon
chr7:52830130-52830354
Coord A exon
chr7:52829607-52830129
Coord C2 exon
chr7:52829476-52829606
Length
523 bp
Sequences
Splice sites
5' ss Seq
TATGTATGT
5' ss Score
3.25
3' ss Seq
AGTTGTCTTTCCTTCCCCAGTGC
3' ss Score
9.5
Exon sequences
Seq C1 exon
AAACTGGTCATTTTCTGAATATCAAGCCTCAATCTCAGTTGGAACAGGGTGAATACAAGGTGGTCCTGAGAGTTGCTGATCGGGAGGGTGAATCTCAGGAGAATATTATTCAAGCAAGTGTGTGTGACTGCAAAGGAGAGGCATTCCAATGTACTGATAAACAAGTAGCAGGGATTCCACTGTTTGGAGTTCTTGGTGTCCTGGGAGGAATCTTACTTCTGCTAT
Seq A exon
GTATGTAACTTTTTTTTTTTTTTTTTTCTTTTAATTTTTCTTTGTTTGCTCTTGTATCTTTACTTCTGTGCATTTCAGTCAAAAAAGTTAATTGTAACTTGTGGCTTTTTTGTGTGTGAGATGTGACCTCTGTAGTGCTGGGCGATATGGCAAAAAAATTATAACGATAATCTTTCATATCGGTCTATATCGATATTTATCATGATAAACGTAAAATCTACTGAAGTCTAGTGACGTTTCTAGTCAGCAATGTCTGTGACTGACCTTTTTTACCTTATTTTTTTCTTACCCCAAGTGAAACATACACTATTACTGTAAACTTTTATTCTGTGTGCGGCACTCGGAAGGGCAGGCTGCAAAATGCCTGCTCAGCGGTACGCATAGTGCCTAAATATTATTTAGCAATTATTGAACTGTCATTATTTTATCGAAGAAAAATTATCGTGATCATTATCGGTATCGAATTATTGCCCAGCCCTACCTCTGTATACTGCTCATTTTAAAGTTGTCTTTCCTTCCCCAG
Seq C2 exon
TGCTTGCTCTTCTTCTGCTCATGTTCCTGCGGAGGAAAAGCAACTCCAAAAAAGAACCGCTCCTTCCAGAAGATGATGTACGGGACAACATCTACTATTATGATGAGGAAGGCGGTGGAGAAGATGATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000102750:ENSDART00000167882:13
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=0.159
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(46.6=53.9)
A:
NA
C2:
PF0104912=Cadherin_C=PU(40.2=75.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTGGTCATTTTCTGAATATCAAGCC
R:
TGATCATCTTCTCCACCGCCT
Band lengths:
353-876
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]