GgaINT0009833 @ galGal4
Intron Retention
Gene
ENSGALG00000005102 | CDH4
Description
cadherin-4 precursor [Source:RefSeq peptide;Acc:NP_001004391]
Coordinates
chr20:7988385-7989630:+
Coord C1 exon
chr20:7988385-7988618
Coord A exon
chr20:7988619-7989396
Coord C2 exon
chr20:7989397-7989630
Length
778 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAAT
5' ss Score
6.41
3' ss Seq
GTCTGCCTTGGTCGCTCCAGGTG
3' ss Score
8.7
Exon sequences
Seq C1 exon
GTATACCCCCAGCCAGCGGCACTGGCACTCTGCAGATCTACCTAATCGACATCAACGATAATGCTCCTGAGCTCCTGCCAAAGGAAGCACAGATCTGTGAAAAGCCAAACCTGAATGTCATCAATATCACAGCCGCAGATGCTGACATCGATCCAAACGTTGGGCCCTTTGTCTTCGAGCTGCCAAGTGTGCCATCTGCGGTGAGGAAGAACTGGACCATAACACGACTGAATG
Seq A exon
GTAAATGGAGCAGGCAATCCTAAGGACATTTGGGCTCTGATTCACTAATGAGGCCACGTGCAGTTTCAAACTTCCAAACTTTCTGACTTTTTTATCTGATTTTTATTTTTTAAAGCACATTATGGCTGACATTATAGACAAGATAGTTAATCAGAAATGATTTGTATCAGACCTGCAGCATAACTCTAAGAGCCTTGGCACTTGGCTTTTTTTAATGCAGTTCATAATTATGAACAGTTATCAGTACTGAACAGAGTATAAATCATCCATAATGGCCAAGGGGAAAAAAGCTATTATCAGTCTTCCTTATGTTCCAGTGTAATTGTCATAAGCCACAATCAGGATCAATGTTCATTTCTCTGACCATAATTGCATAAAGGCAGCCTTTTAATTTACCATAGAACCAGGAGGGCTAGGTAAGTGTGAAGATTACCAGTATGTGAAGGATTTTTATATTGCAGCATGCAACCACAATTGGCCCTAATTGCTCCTCTGATTAGTGGTAGTTTAAGCAGAGGATTGAAAACACTGTGGAGCCCAAAGGCTGGTTTTGCCTTCAGAGCTGGTCTCCATCACTGAGAGGCCTGTGTCTGTGTGATTTGAGGCTCAGCCCCACACCTGTGGTACCCAATGGGAGGGAACTTGAGAAGGATTAACACAACTGAGCAGGTCGTGGATGGGGTTTGGGCTTCCCAAATCCCCCGAGGAGGGTGGGCATGGCTTTGTGAGCCGTGGCTCTCCGTGTCTGCCACACATTTGTCTGCCTTGGTCGCTCCAG
Seq C2 exon
GTGATTACGCCCAGCTTAGTTTACGGATCATGTACCTGGAGGCCGGTGTGTATGATGTGCCAATCATAGTGACAGACTCGGGAAATCCCCCCTTGTACAACACGTCCATCATCAAAGTGAAGGTGTGCCCGTGTGACGAGAACGGTGACTGCACCACTATTGGGGCGGTGGCTGCTGCAGGACTGGGCACGGGAGCCATCATCGCCATCCTGATCTGCATCATTATCTTACTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005102:ENSGALT00000008180:11
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=0.000
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(15.8=19.0),PF0002812=Cadherin=PU(54.3=64.6)
A:
NA
C2:
PF0002812=Cadherin=PD(44.7=53.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTCATCAATATCACAGCCGCA
R:
ATGATGCAGATCAGGATGGCG
Band lengths:
342-1120
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]