GgaINT0033673 @ galGal4
Intron Retention
Gene
ENSGALG00000006039 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr9:4402297-4403681:+
Coord C1 exon
chr9:4402297-4402359
Coord A exon
chr9:4402360-4403497
Coord C2 exon
chr9:4403498-4403681
Length
1138 bp
Sequences
Splice sites
5' ss Seq
CTAGTGAGT
5' ss Score
7.43
3' ss Seq
TCTCTGCTCGCTCCGGCCAGGAC
3' ss Score
7.86
Exon sequences
Seq C1 exon
TCAAACGCAACGTGAACAACAAGAATGATATCAGCAGGCCTGTCATGCTCACCACGCGCACTA
Seq A exon
GTGAGTAGCGTCCTCAAGGGAATTAGGTTGTGAGTACAGGCCCCCCAGTGCCTGGGGCACTGCTCCCAGCCCGCTGCCCTCCCCACGGCCGCCTTCGGCTTCCCGTGTCCTGGAGGTCTGCTCCAGCCTGAACCTGCTGGCCGTGGTGCGGCTGAAAAGGTGGTGTGCAGGCCCTGAAGTCCTGGGTTGAAAGTGCTTGGAGTAGATGGGTTTTGTTTTTTTTTTTTTCCTCTTTTCTGTGGCCAGTGAGAGCAGGGTCTGAAAAGAGTAGCCAAGCCCTCTGGGGCTGGTGCGGGTTGTCTGTGCCCGCAGCATCATGCTGCGCTTGCTGTTGGGGTCTGGGCCTGGCAAAGTCTCATTGCGGGCTGGGCGGTGAGGCTGGAGTGCCCAACAGAAGATGACCACTGTGTTGCTTTCCGGGGTCCGGCGTGCCTCAGCGGGCACAGGAGACCTCTGCTCTGTGGGTGGGGGCAGTGAGGCAGGATCATAGCTTCCTTGGGCATGGACCATTGTTGTGGGACAAGCAGATGCTGCTGCATCCTCTGTAATGCGTAATCCCTGGCCTGTGGATGGCTGGAGCATAAATCGAAGGCAAATTGAGGATGAAAGAGATTGGACCTGGAAAAAATTCCCTGTAGTGAGAGGGGAGGCCCAGGGGCTTGATCCCATTGCTGGTGAGCTAGGCTGAGCCCAGCGCTGCCCATGCGTGGCACCAGCCCAGAGGTGACCTGGAGCAGGGCCTGAGGGTGTGGGGCAGCCGGGCAGCCTCTGCCGCTGGGTTAGCCTTGGGTCTAGGCCTCATCCATGCTGGTGTGCACGTGGCTGGGTGGAGGCTAGAGGCTGGGCAGGCAGCACCAGGCCTAAGGGATGACTACGAGCTGGACCCCTGGGCTCCATGCTTGCTGAGGAGCAACCAACATGGGGGCCAGGCTGGGTGCCCCCGGCTGCCCAACAGCGGGGACACGGGGCAGTGGCGCTGAGCCGTCCTGGTGCTGTGGATGTGCCCATGGTGACTCTAGGAAGGCTGGTCCACATGGCAGGCTGGGGCGTGGGAGATAAGGGATGCGGGAAGGATGCAGCCCCGCCGCGGCCAGCTGCTGACCGCAGCCCTCCCTGCTTCTCTGCTCGCTCCGGCCAG
Seq C2 exon
GACCGCGTCCGGTGGAAGGCTTTGAGATCACGAACGTGACGGCCAGCACCATCACGGTGCAATGGGCTCTCCACCGGCTCAAACACTCCACCGTCAGTAGGGTGCGTGTCTCCATCCGCCAGCCTGGGGACCTGGAAGACCGCACGGTGGAGCTGAACAGCAGCGTGGCCAAGTACACCTTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006039:ENSGALT00000009725:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.710 A=NA C2=0.290
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(17.4=80.0)
A:
NA
C2:
PF0004116=fn3=PU(69.8=96.8)
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:
TCAAACGCAACGTGAACAACA
R:
GGAAGGTGTACTTGGCCACG
Band lengths:
246-1384
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]