GgaINT0033656 @ galGal4
Intron Retention
Gene
ENSGALG00000006039 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr9:4393567-4394822:+
Coord C1 exon
chr9:4393567-4393729
Coord A exon
chr9:4393730-4394696
Coord C2 exon
chr9:4394697-4394822
Length
967 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
GGGCGTGCGTGTCTCCGCAGCCT
3' ss Score
7.71
Exon sequences
Seq C1 exon
GCAGGTTTTAACGCCGGTGATGGAAAGCGCTACTTCAACATCCCCGGATCCCGCACTGACGACATCGCTGACGTGGAGATGACGACAAATGTGGGTATCCCCGGGCGCTGGGTGTTCAGAATCGATGATGCCCAGGTGCAAGTGGGGGGCTGCAGCAATACAA
Seq A exon
GTAAGAGGACAGCAGTTAGGTTTATTTAACTCCCAACCCGATCCCAAACTGTTCTCCAGCCCTATCTTTCCCTGCCTCGATCCCCACCCTCACTTTCCCCCCCTGAGGGGAGAGAGCAGTGACCCACGGGTGGAGCAGACAGCTCGAGGGGCTCGGGGAGGGCTCGGGGTGGGGGCAGCAGTGGGGACACCGTCCTTGGAGCCGCCAGCCCCCTGCGTGGCTGTGGGAAGCGTGGCTCCCGGGCTCTGTGCCTGGGGATCCCCGGTCTGGTTGGGATCTGCCCGCTCGTGCTGGGGTGGAAAAAGCCAATGGGGAGGAAAGCTCCTGAGACCAATACAGGCTGCGGGGTACTGGGGAGGAGGTGAGGGGGAACGTGAGGGGCTCTGTGGCCCCGGCACCACTGTGGGGCTGGGCTGTCACCCTTAGGGCAGCTCGTCTGTCCTGTGGGGCCTCAAGGCAGCCGCTACCCAAGGAGGCCAGCAGTACACAGGGACTGTGCCCAGCCATCCTCCACGGAGCCACTGGCCTCCTGTTCCTTGTCCCTGCCCCACCCTGGCCGTGTTTTCTTACCCGCTAATCTACGCGTGTTTCATATGACCTGTGGGTTTGCTTTGGACAGGTTCTCCCATCCCTCTTCCCCTCTGCCCCGGGCCATAGGCAAGGGCTGGCTGGATAACATCCGCTGGTTGTCCCTGCCTGGTAGGGCTCTGGCCCTGCCTCCCCGCTCCTGCAGCAAGATTAAAACCTTCACCCTGCCCGAGAGCAGCGAGCCCATCTGTGGGGCACACAGCCCCCAAGTGCGGGCTCCCCAAGCTCCCTGGAGAGCCGGGTGACCATATCCAGCCCAATGCACGGACGGCGGGGCTGGATGGATGCTGGGACGGACCCCGGCGGTTGCGTGGCCGGAGTGCAGCGTGTCAGCCCAGCCGGAGCGGGCTGTGAGCGGAGGGCGTGCGTGTCTCCGCAG
Seq C2 exon
CCTCCGTGTGCCTGACGCTGCGGCCCTGCCTGAACGGGGGGAAGTGCATCGAGGACTGCATCACTGGGAACCCCTCCTACACCTGCTCGTGCCTCGCGGGCTTCACAGGGAAAAGGTGCCATGTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006039:ENSGALT00000009725:4
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=PD(47.3=78.2)
A:
NA
C2:
PF0000822=EGF=WD(100=83.7)
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:
AGGTTTTAACGCCGGTGATGG
R:
GACATGGCACCTTTTCCCTGT
Band lengths:
286-1253
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]