GgaINT0033672 @ galGal3
Intron Retention
Gene
ENSGALG00000006039 | SNED1
Description
NA
Coordinates
chr9:5945032-5945875:+
Coord C1 exon
chr9:5945032-5945145
Coord A exon
chr9:5945146-5945578
Coord C2 exon
chr9:5945579-5945875
Length
433 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
CTTTTGCCCACACCCTGAAGAAT
3' ss Score
3.21
Exon sequences
Seq C1 exon
CCAGTGACCCGTGCTTCTCCAGCCCATGTGGGAGCCGAGGCTACTGCCTGCCCAGCAATGGCACCCACAGCTGCACCTGCAAAGTGAGCTACACAGGCAAGAGCTGCGAAAAAG
Seq A exon
GTAAAGGCCCTGAGCAGCAGCACCAGGACGTGGCGAGGGGCTAGCCAGCAGTGTGCCTGCCCTGTCACCCACCATCAAGGGGCTCGGCCGTCGGGGACCGGCAGCTCTCCTCCCCCTAGCAGGGCTTGGATCTCACCTCTGCCAGGGGAGCCCAGGCTCTGTGGATGCNNNNNNNNNNGTTCCTAACTCAGCCGTGCAGGCTGTCTGCTTGCCCTGGCTCTGTTCAGGCCCATTGGGGTGGCTGAGCAGCCCCGGCTCCTCCAGCACACGCTTGGCACCTGGCACGACCGGCCGGCGGCAGCCATAGGGCTTCTGCAAGCTGCAACGCGAGCGAGAGAGGACCCTGTCCTCCATCTGCATTTCATTGCTGGGGTCTGTTCTCTAAAGATTCATGGCATTACCTCTCCCCTTTGCTTTTGCCCACACCCTGAAG
Seq C2 exon
AATTGCTGCCACCAACCTCATTAAAGGTGGAAAGGGTGGAGGACACTGGTGTGTTGATTTCTTGGCACCCTCCTGAGGACGCAGCCGCCAGGCAACTCATTGACGGCTACGCCGTGACGTACGTATCCTTCGACGGCTCTTACCGCAGGACAGATTTTGTGGACCGAAGTCGTTCTGCCCACCAATTGCGGGCACTAGCCTCCGGCAGAGCCTACAATATTTCTGTCTTTTCAGTCAAACGCAACGTGAACAACAAGAATGATATCAGCAGGCCTGTCATGCTCACCACGCGCACTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006039:ENSGALT00000009725:20
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=0.120
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=79.5)
A:
NA
C2:
PF0004116=fn3=WD(100=84.0)
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:
CTACTGCCTGCCCAGCAATG
R:
GCATGACAGGCCTGCTGATAT
Band lengths:
356-789
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]