GgaINT1008872 @ galGal4
Intron Retention
Gene
ENSGALG00000026291 | CDH3
Description
cadherin 3, type 1, P-cadherin (placental) [Source:HGNC Symbol;Acc:HGNC:1762]
Coordinates
chr11:18315399-18315927:+
Coord C1 exon
chr11:18315399-18315623
Coord A exon
chr11:18315624-18315708
Coord C2 exon
chr11:18315709-18315927
Length
85 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACG
5' ss Score
9.65
3' ss Seq
TTGTCGCCTATGCCGTGCAGGTG
3' ss Score
5.61
Exon sequences
Seq C1 exon
GATTGCCACCCGCCACAGGCACCGGCACGCTGCTCCTCACCCTGCTGGATGTCAATGACCACGGCCCTGAGCCGGAGCCCCGCGACATCGTCATCTGTAACCGCAGCCCTGTGCCTCAGGTGCTGACCATCACCGACCGGGACCTGCCCCCCAACACCGGGCCCTTCCGTGCCGAGCTGAGCCACGGCTCTGGGGACAGCTGGGCGGTGGAGGTTGGCAATGGAG
Seq A exon
GTAACGTGGGGACTCGAGCTGGTGGCACACGTGGTCCCACATGAGCCAAGGTGGCGAAGTCAAGCTTGTCGCCTATGCCGTGCAG
Seq C2 exon
GTGACACCGTTGCCTTGTGGCTGACGGAGCCCCTGGAGCAGAACCTGTACAGCGTCTACCTGCGGCTCTTCGACCGCCAGGGCAAGGACCAGGTCACCGTCATCAGGGCACAGGTGTGCGACTGCCAGGGCCGCGTGGAGAGCTGTGCCCAGAAGCCACGCGTGGATACGGGTGTGCCCATCGTGCTGGCCGTGCTGGGTGCTGTGCTGGCCCTGCTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000026291:ENSGALT00000000855:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.382 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(15.8=19.7),PF0002812=Cadherin=PU(54.5=63.2)
A:
NA
C2:
PF0002812=Cadherin=PD(44.3=52.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCAGGTGCTGACCATCAC
R:
GACGCTGTACAGGTTCTGCTC
Band lengths:
168-253
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]