GgaINT0033655 @ galGal4
Intron Retention
Gene
ENSGALG00000006039 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr9:4392587-4393729:+
Coord C1 exon
chr9:4392587-4392727
Coord A exon
chr9:4392728-4393566
Coord C2 exon
chr9:4393567-4393729
Length
839 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
TTCTGCCCTTGTCCTCCCAGGCA
3' ss Score
10.71
Exon sequences
Seq C1 exon
GTAAACACATTCCAGATCGTCCTCATCACGGACGGCAAGCTCTCCTTCACCATCTTCAACTATGAGTCCATCACCTGGACCACGGGTATGCACGCCAGCAGTGGGGGGGACTTTGCTGGGCTTGGCGGCATCGCAGCGCAG
Seq A exon
GTAAGCAGCGGACACGGCCATCACCCCCAGGCAGTGCCCGAGCCCACCGCACTCAGTGCTCTTGGCCTTCCCCGGAGCCGCTCTGGCAGCGCGGTGCGGCCCATGGATTTTTGGTGGTGGCTCCCTCCCTCCCCCTGCTTTCTTAAAGTTCTTAAATATCCATCTGTGCTCTCGTTCCCGAAGCTGAGACCATATAGGGGACTTTGTTATAACGAAACCACGGTTCTTTACCTTGGCTGCTGCCTCTTAGTTCCTTTTCCTTCCTAACCTCAGACTTTAAGAGCAGCCCGTCAGCTGCCGCAGCCAGCACAGCTTTCGCTTGTATTTTTATTTCATCCTTGTGTGCGTTGTTGTGTTTAAGAGGGGAAAAAAAACCGCAACCCAGTCCCCATTCGGATGTGTGAATTTACCACCAGTTGATCTGTCCTTGGCTCCCCGCCTGCCCGCCTGCAGGAAATCGCAGGTGTAGAGGAAAGAGACACGTTTTGAATCCCCGAATTCAGGAGCAGGGTGGGTTTTATGAACGTAAACAGAGCAGTGGCAGCACACCTTGGCCAGTGAGCAGCCTTCCGGGAGCTCCTGCGAGGAGGAGTGGAACCTCAGGGGAAGAAACGTCCTTCTTACCCCGTGCCTCTGGGCTGTGGGTGCTGTGAGCCTGTGCTCCTGGGCACGGGGAAAAGCAGTCATCCCAGGGGATGATCCATCACTGCAGGGATGCAGTAAGAACCCGGGTGGTGGCGGCGGTGCGCGGTCCAGCAGCGCACCCCCTCGTGCCGCGGCCCCTCGGGTGCTGTTCTGAGGTATTGATGGCTCTTTGCTTTCTGCCCTTGTCCTCCCAG
Seq C2 exon
GCAGGTTTTAACGCCGGTGATGGAAAGCGCTACTTCAACATCCCCGGATCCCGCACTGACGACATCGCTGACGTGGAGATGACGACAAATGTGGGTATCCCCGGGCGCTGGGTGTTCAGAATCGATGATGCCCAGGTGCAAGTGGGGGGCTGCAGCAATACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006039:ENSGALT00000009725:3
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:
PF061199=NIDO=PU(50.5=97.9)
A:
NA
C2:
PF061199=NIDO=PD(47.3=78.2)
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:
AAACACATTCCAGATCGTCCTCA
R:
TTGTATTGCTGCAGCCCCC
Band lengths:
302-1141
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]