GgaINT0026005 @ galGal4
Intron Retention
Gene
ENSGALG00000000608 | CDH1
Description
cadherin-1 precursor [Source:RefSeq peptide;Acc:NP_001034347]
Coordinates
chr11:18324313-18324741:+
Coord C1 exon
chr11:18324313-18324534
Coord A exon
chr11:18324535-18324610
Coord C2 exon
chr11:18324611-18324741
Length
76 bp
Sequences
Splice sites
5' ss Seq
TGAGTGAGT
5' ss Score
6.51
3' ss Seq
GCCATGCCCTCTGCTCGCAGTCC
3' ss Score
8.9
Exon sequences
Seq C1 exon
ATGAGCTGGCCATGGGCCTGAAAAAGGAGCTGGAGCCGGGCGAGTACAATATCTTTGTGAAGCTGACGGACAGCCAGGGCAAGGCACAGGTGACGCAGGTCAAAGCCCAGGTGTGTGAGTGTGAAGGGACAGCCAAGAACTGCGAGCGGAGGTCGTACATCGTCGGTGGGCTGGGTGTCCCCGCCATCCTGGGCATCCTGGGGGGAATCCTGGCCCTGCTGA
Seq A exon
GTGAGTACGGTGTGATGGGGATGTGGATGGGGCTGCTTTCCCCTCGCGGCCCTGATGCCATGCCCTCTGCTCGCAG
Seq C2 exon
TCCTGCTGCTGCTGCTGCTGCTCTTTGCCCGGCGACGCAAAGTGGAGAAGGAGCCGCTGCTGCCGCCCGAGGATGACATGCGGGACAACGTCTACAACTACGACGAGGAGGGCGGCGGCGAGGAGGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000608:ENSGALT00000000857:13
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=0.591
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(43.7=50.7)
A:
NA
C2:
PF0104912=Cadherin_C=PU(22.3=75.0)
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:
AGGTGTGTGAGTGTGAAGGGA
R:
CTCCTTCTCCACTTTGCGTCG
Band lengths:
167-243
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]