GgaINT0026004 @ galGal4
Intron Retention
Gene
ENSGALG00000000608 | CDH1
Description
cadherin-1 precursor [Source:RefSeq peptide;Acc:NP_001034347]
Coordinates
chr11:18323886-18324534:+
Coord C1 exon
chr11:18323886-18324110
Coord A exon
chr11:18324111-18324312
Coord C2 exon
chr11:18324313-18324534
Length
202 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
TCCCCTCTCCCTTCCACAAGATG
3' ss Score
7.21
Exon sequences
Seq C1 exon
GGATACCGGATACCACCGGTACGGGGACGCTGCTGCTGCTCCTCCAGGATGTGAATGACAACGGGCCCACCCCAGAGCCCCGGTCCTTCGAGATCTGCAGCCGGCAGCCTGAGAAGCAGATACTGAGCATTGTGGACAAGGACCTGCCCCCACATACCTACCCCTTCAAGGCAGCACTGGAGCATGGTTCCAGCAACAACTGGACTGTTGAGATAAGGGGCCAAG
Seq A exon
GTAGGTGCTGTGGGGTGCAGGGCAATGAGGGGACACTGAGCAAGGCACAGATCCCAACCACTTCTTTCCGTGCTACCCTGAATGCCACCAGCACCGAGCTTCTGCTGGCTTGCATGATGGGGAGCTGCCATGGGGCAGAGCCCTGATAGTGTCCCCACACCTGGGGACAGCTCTGAGCCCAATCCCCTCTCCCTTCCACAAG
Seq C2 exon
ATGAGCTGGCCATGGGCCTGAAAAAGGAGCTGGAGCCGGGCGAGTACAATATCTTTGTGAAGCTGACGGACAGCCAGGGCAAGGCACAGGTGACGCAGGTCAAAGCCCAGGTGTGTGAGTGTGAAGGGACAGCCAAGAACTGCGAGCGGAGGTCGTACATCGTCGGTGGGCTGGGTGTCCCCGCCATCCTGGGCATCCTGGGGGGAATCCTGGCCCTGCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000608:ENSGALT00000000857:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.237 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(15.8=19.7),PF0002812=Cadherin=PU(55.2=63.2)
A:
NA
C2:
PF0002812=Cadherin=PD(43.7=50.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGATGTGAATGACAACGGGC
R:
CTTCACACTCACACACCTGGG
Band lengths:
306-508
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]