GgaINT0033669 @ galGal4
Intron Retention
Gene
ENSGALG00000006039 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr9:4399374-4400527:+
Coord C1 exon
chr9:4399374-4399487
Coord A exon
chr9:4399488-4400413
Coord C2 exon
chr9:4400414-4400527
Length
926 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGA
5' ss Score
8.91
3' ss Seq
AGCACATCTCCTCTCTGCAGAAG
3' ss Score
8.21
Exon sequences
Seq C1 exon
AGATTGATGAGTGCCGGTCTCAGCCCTGCCTGAACGGTGGCCAATGCAAAGACCGCATCGCCGAGTTCCTGTGCGTGTGCGAGCCGGGATACACGGGCCTCCACTGTGAGTTGG
Seq A exon
GTAAGAGAATGCACAGAGCTCACGTGGGGAGCAGAGGAGGGAGTCCCCATGGGTGGCTGTCCCCGCAGGTGGCTGTCAGTACAGCTGGAGTCATGCAGCTGGGAGTGGGGCTGCCTGTGTGCCCCAGCTCCCATCTCCTGCCCACTTGCGGCTCAGGGGAGCCCCCAGCCCACCTGGGGTGGGTGCACGTGCTGCTTGTCCATCCATGCCAATGGGTGCTGCACGGACATCTCTGGCGTTGATGGGGCTGTGATTCCCAGGGGGTTGGGTCAGAATCCCCTGAATGGCTTTTGTGTGCCTCCAACACCCCCTGCTTGTCACGGTAGCATTTGCTGGAGAACGGTCCCAACGTGACCTTCATGTTCTGAACATGCGTAACGAAGGCCCAGATAGCAGGATCTGGGTGAGGAGTGTTCCCCACAGCTCCAGAGTTACTGGCCAAGAGGGAGGATGATGAAAAGCAGCTTAAGATTTAACCTTTTCTGGGTGCAGAGTGGGCTGTCCCTCCCACAGCAGTTCCTTGCACTTGCTCTCCTCTGTGCATGTGTTCATTGTGGCACAGGGGCTCTGTTGCATGCTGTTTGGTGGGTGCTGGTGGGAGGGGTGTCAGGTGGCACAGGGGCTGGTGGGGCACTGCACAGCTGGGTGATGGGGTTAGCTGGGTTGGATGCAATGCCTTCAGGAGGGGATTGAAGGACAAGATGTACCATGCACACCTTATTTGTGACTTGTGGTGTCTCGGCACAGCTCCACAGCACCAGCTTTCCCCATCCGTGTTGCCCCTCTGTCCAGCCCCATGTGGGGCTGTCTTTGCCCGGGGGAGTTCAGGGCAGTGAATGACATGGGGAGGAGAAATGGCATCTCTCCAGACTTTTTGTTCTGCCTGCCAGCCCTGGCTCTGCTCTGAGCACATCTCCTCTCTGCAG
Seq C2 exon
AAGTTGATGAGTGCCAATCAGAGCCCTGTAAGAACGGTGGCACCTGCCGGGACCTCCTGGGCTCCTTTGCCTGCTCCTGTCCCGCGGGCTTCATGGGCACCCAGTGCGAAGAAG
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATTGATGAGTGCCGGTCTCA
R:
CACTGGGTGCCCATGAAGC
Band lengths:
219-1145
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]