GgaINT1026037 @ galGal4
Intron Retention
Gene
ENSGALG00000006039 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr9:4405584-4406112:+
Coord C1 exon
chr9:4405584-4405700
Coord A exon
chr9:4405701-4406024
Coord C2 exon
chr9:4406025-4406112
Length
324 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGT
5' ss Score
8.83
3' ss Seq
CTCTCCTGTTCCCCAAGCAGCCT
3' ss Score
6.47
Exon sequences
Seq C1 exon
GCATCAGGCAGAACTGCTCCACAAACCCCTGCAAGAATGGAGGCACCTGTGTAAGCGAGAGCGAATCCTACCATTGCGACTGCATCCCGGGCTTCAAGGGCAGGCACTGTGAGCTAG
Seq A exon
GTGAGTGCTGTGCTGCTGCAGGGTGTGTGACAAGGCTGAGAGCTGTCCCAGCAGCGGGGTCCCACAGGGCACAGGTCACTGAGCAGCCCCATCCATAGCCGGCTCCCGGGTTCTGGCTGAGCCTCCAGCAGCCGGGATCCTGCTGTGCCCTGCAGTACCACTAGGCTGGAGCTCACTTCTGGCGGGTCGGCTCCGAGTGACAGAGCCTGCAGCTCCAGGACTGCAGTGTGGGGATCCTGGGGGGCCTTGATGGCTTCCGGGGCACAGGCAGGCAGGGCCTGAGGTGGGCTTGCTGATAGCTCCCCTCTCCTGTTCCCCAAGCAG
Seq C2 exon
CCTGCAAGAAGGTGCCACACTCGTGCACGCGGCTGTACTCGGAAACCAAGTCATTCCCTGTGTGGGAAGGAGGCACCTGCCACTACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006039:ENSGALT00000009725:29
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=77.5),PF055076=MAGP=PU(31.2=62.5)
A:
NA
C2:
PF055076=MAGP=FE(36.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACTGCTCCACAAACCCCTG
R:
TGCCTCCTTCCCACACAGG
Band lengths:
182-506
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]