GgaINT0033670 @ galGal3
Intron Retention
Gene
ENSGALG00000006039 | SNED1
Description
NA
Coordinates
chr9:5944237-5944932:+
Coord C1 exon
chr9:5944237-5944350
Coord A exon
chr9:5944351-5944818
Coord C2 exon
chr9:5944819-5944932
Length
468 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGG
5' ss Score
8.76
3' ss Seq
CAGCCTGCTCTCTCCTGCAGAAG
3' ss Score
9.9
Exon sequences
Seq C1 exon
AAGTTGATGAGTGCCAATCAGAGCCCTGTAAGAACGGTGGCACCTGCCGGGACCTCCTGGGCTCCTTTGCCTGCTCCTGTCCCGCGGGCTTCATGGGCACCCAGTGCGAAGAAG
Seq A exon
GTAGGGACCCTACTGGGCAGGGACTGTCACTTGGGCTCGGGGCATGGCCAGCACCTGTGCCTAGGCAGCTGCTGGGCGTCTGTCGCAGGGTTGGCACTCAGTCTCGGCCACTGTTGAGGGTACGGACTTAACCTTGACCTGGAGAGGACGCTGCTGTCCGTGGCGCTCACTGCATCTTGTGTCTGCCAGCAGCAGAGCTGACACTTCTCCCAGTGGGGGGAAGGAACAGCCCCAGCAGAGGACTCGGGCCTCGTGCCTGTGAGCTGCCTGTCTGCTTGGCAAGGCAGTGCTGTGCCAGGGATTGAGGCCACCGTGGCATTGAGCTGGGGATTCTGAAGGTGGGCTCTGGCTGGCAGCCCTAGGCTACACCTTTGTGTTGCTGCTGTGGTCACACGGGGGGCTGGCTGCCAGCACATCAGCTCGCTGCCTGCTGCAGGTGCTTTACTTCCAGCCTGCTCTCTCCTGCAG
Seq C2 exon
AAGTGGACGCCTGTGAGTCAGACCCTTGTCAGAATGGAGGGGAGTGTGAAGGTGATGGAGGTTCCTACCTGTGTGTGTGCCCAGAGGGTTTCTTTGGTTACCACTGTGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006039:ENSGALT00000009725:18
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:
PF0000822=EGF=WD(100=79.5)
A:
NA
C2:
PF0000822=EGF=WD(100=79.5)
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:
GATGAGTGCCAATCAGAGCCC
R:
TGTCTCACAGTGGTAACCAAAGA
Band lengths:
222-690
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]