GgaINT1026030 @ galGal4
Intron Retention
Gene
ENSGALG00000006039 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr9:4388903-4391801:+
Coord C1 exon
chr9:4388903-4389109
Coord A exon
chr9:4389110-4391513
Coord C2 exon
chr9:4391514-4391801
Length
2404 bp
Sequences
Splice sites
5' ss Seq
TACGTGAGT
5' ss Score
7.77
3' ss Seq
TGTCCCCCCTTCGTCTGCAGGTG
3' ss Score
13.48
Exon sequences
Seq C1 exon
ATGCGGGGCCCGGCGGGCTGGGTGGCGCTGGCGGCGCTGCTGGGCGAGTGGCTGCGGGCGGGCGGCGTGGTGCCGCTGGCGGACTTCTACCCGTTCGGGCCGGCGCAGGGCGACGCCGCCACGCTGAAGCAGGACGACGGCGGCTCCGAGCTGCGGCCCCTCTCCGTGCGCTTCCCCTTCTTCGGAGCGGGGCACACCGGGCTCTAC
Seq A exon
GTGAGTGCCGGGCCGCGGGGGGCCCGCCGAGGGGGGGAGCGGGGCAGGCGGGGCTGCGCCGGAGTCCGGGGCTGCCGGCTGCCTTCTCTCCCTCCGAGCCCCTTCTCTTGCCTGTTTGCTTTTCTTTCTTATTAATTAACGCTCCGCTCACACCGCTCCCGGTGCGTCCCTCGGACGGGTGGCTGCGTGACCTCTATTGAATGCAGAGCGTCGGAGTCCTCGACCCCAAAGCTCAGCCTTTTAGGGGAAAGGGGACCGAGCGGAGGCGGCTGCTGTGCCGGGCGGTGCCGGTGGGGCCGGGCAGCGCCGCTGGAGCAGATGTTGTGCGGTCCCGGGCCGTGAGCTGAGCGGCAGATGTGGGACGTGCCTGCTGCTCTCCATGTGCGAGTCATTAATTGGGCTGACAGGACGCACTGGCATCTGCCGAGCATTCTAAAATTGCGTTTCCTCCGAGGGCTGTACAACCTTCTGCTTGCCATGCCGTTCCCACCCGGGGATGCTGCTGTGTGGCACTGTCCCGTGCAGCTCTCGGGCCGTCAGCTCTCAGGATGGGCTCCCATGGGGGCAGAGCATCGCTGGGCAGCACCCAGCAGTGGAAGCATGTCCGTGTCCCCATCCCTCTCACCATGCTGGCCGGCCTCCAGAAGGCTTTCGTTTCTGCTGACACCGAAAGCACCACGATCACGCTGGTCCCTCAGGGAGGCGCAGGCAGATAGCCTGACCACAGTCACACTTCGGTGCCAAGCCTTGAAGCCAAGGCCCTGGGAAGGAGCAATCGCTGTGCTTGTCTTGGGCTGACCCAGCAGTGTGGTGGGGATGAACCCTTGACTGCTGATGCTTCCTCTCAGAGTGTCATCGAAGCAGTGAGAGGTGGTCCAACAGCCTTCGAGGGAGCTGGCATTTGGGAATGCTCTGTGCAGAGGCCGGGGGACCTGGCACAGCGAGGAGGGTTGTGCAGGCTGCTGGGCGTGGCAGGGTGTTGCCTAACACACAGGAAGAGATGGGCACGGCACAGGGGCTTGCTGCGACCTGTCCCGTACTTCCCCCTCTGGCGCCCAGCCTGCAGTATGTCTGTGCCCTGGGCAGCCTGGCAGCTTGGGATCCTGCTTGGGACCCTGCTGGGGACAGCCCAGTTTGGAGCAGCTAGCATGCAGGGTGTCCTGTGGGCAGGGGGCTGGAGAAACCCAGCTCTGTTGGGTTGAAGGAGTAGGGAAAATGAGCGGGTGTGGGTTTTCCGGTGTGTAGTAAGCATCGTGTCATGCTCCTGTGCTTTTGGAAGATGGGTGTCTCGGTGGTCTCGTCCCATTTTTCTGATGTGGTCCAAGTTGACCGAGAATTCACAGCAGATTGATGGGGCACACCAAGATCTGTGCCTGTTCCTGCTGGGATGCTCCCGTCCGTTGTCTCAGCTGGGAGCACGCGTTGCTTGGACCTCGCTGGTTCAACCTCGTGTGTCTTTGGCACAGGGATTTCTCTGGGATGAAAACGCCGGCCCTATGGCAGCTGTGGGAGATGCACTGTCCTCGGGGCCAAGGGGCTTTGGTGTCTGCCTTGAGGGGGGGTGGTCCTGTAGGGGTGGCTGTCACCTCACATCTCCAGGGAGCCACACAAGCCGCGGCCAAAGCACAGGGCCCAAAGTGCAGAGCTTGACCCTGGGGGTCCCTCTGGGCCTGCCCCTTCCTCTGTAAAACAAACAAAAAAACCCTTTCTTGGCACTAACTCTCTCCCATCTTGCTTTAATAAGGGGAAGAATGTTCCTCTGCGGACACTGTGAGGTTACGGAGGGTTTTCTGAAAGGGAATGGCGTTCCCCTCAGTCACAGCAGGGCCTGCCCTGGGGCTCTTGGGACCCTACAAATGGCCGCAGCCAGCATGAGGGGCTGCTGGGGGCTGCGAGGCTCTGCAGGGCAAATCAGCCCCCCTGGAATTGTCACACCTGCGTGCCCACACCTCCCCGGCCTCTAACAGAGTTCATCAGCCCTGGGAGCATAGAGCCCATGAGTGTGGGCACCCCGTGCTGGTAGGCCTCAGTGGGCCGGCGGTGCTGGGTGCCGCTGGTTAGCCAGCCCAGACTGCGGCTGTGGGTGCCCCCGGCCCAGGCGGGTGCTCTTTCTTTTCCTGCCAGGCCTGGCCAGGCTGCGGCGGGAGAACAGGGCCGGGTTTGTTCGGTGGAGGTCGGGGGGTGAGGCCACTTTCCCGGCCGGGCCGCCCGTGCTTCAAAGGGCAGGAAGGGGAAACGCTCAAATATTTGTGGAAGGAGGCTGCGGGGGAACGGGCGAAGCAAAAAGTGCCTTTAAAATAAGGATTCAGCGCGGCCGGGGCTGAGAGGGCAGCGGGGGAACGGCCCCATCGGCGCGCCTCAGGGCCGGCACCATCCTTGCCCGCTGTCCCCCCTTCGTCTGCAG
Seq C2 exon
GTGAACAACAACGGGATCATCTCCTTCCTGAAGGAGGTCTCTCAGTTCACACCGGTGGCCTTCCCGATCTCCAAGGACCGGCGTGTGGTGGCGGCTTTCTGGGCGGACGTGGACAACCGGCGGGCGGGCGACGTGTATTACCGGGAGAGCCAGGACCGGGCCATCCTGGAGCGGGCGACCAGAGACATCGCGCGGTACTTCCCCGAGTTCCCCGACTTCTCTGCCCAGTGGGTGTTCATCGCCACGTGGTACCGAGTCACTTTCTTCGGGGGAAGCTCGTTTTCTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006039:ENSGALT00000009725:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.058 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]