GgaINT0125647 @ galGal4
Intron Retention
Gene
ENSGALG00000003509 | C9ORF9
Description
chromosome 17 open reading frame, human C9orf9 [Source:RefSeq peptide;Acc:NP_001264636]
Coordinates
chr17:6718225-6718961:+
Coord C1 exon
chr17:6718225-6718427
Coord A exon
chr17:6718428-6718813
Coord C2 exon
chr17:6718814-6718961
Length
386 bp
Sequences
Splice sites
5' ss Seq
TAAGTACGT
5' ss Score
5.1
3' ss Seq
GGCTTCCTTCTGTCCCACAGATA
3' ss Score
10.4
Exon sequences
Seq C1 exon
GTACAGTCCTACATGGACCACCACTGTAACAACTTAACGGACAGGCGTATCCTCACCATGTTCCTAAACATCTGTAATGACCTGAGCAATCTCTGCCACAAGCTGGAAACTCTACATCCTGGTAACAGCACAACCAATGAAATTTTGGAAAGATGCAAGCTGCTCCTTAACCACAGCAATGATCTGAGCACCATCCGAGCTAA
Seq A exon
GTACGTCCTTCTGTCAGCTGAATTCTGTGGAGGCCATTGCTGATACAGGAAGACTGTTGCAAGAATGCATATTCCTACTTGACCTCCCTGTTGGTTACTGTTGTAACACAATTCTGGCTCCTCCCTGCTATTTCTGCTCTGTGTATAGTTAATTTCTGTGGAGCAGGTGTCTGCATGTGCTCTTGAACTCCTGCAGACTGAGGCCAGCAGCCACAATGCCATGTGCGGCACAGCTCCTTTCTCAAGTCCTATCAGTGCCCTTTTGTCCTGGGGACATTGCTGTCTACATCTCCACCCTTCCCTGTGGGCCTCAGGGAGGCACTGCTGGGCTCACCAGGGCTGCATTGCCTGGACTACTCAACAAATGGCTTCCTTCTGTCCCACAG
Seq C2 exon
ATACCCCCACGACGTTGTGAATCACCTGAGCTGTGACGAAGCAAAGAATCACTTTGGAGGTGTGGTGAGCCTCATCCCCATTGTCCTAGATGGCGTGAAGGAGTGGCTATCCCACACTGAGAAGCTGCCACGACGCATGCTGTGTAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003509:ENSGALT00000005551:3
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=0.080
Domain overlap (PFAM):
C1:
PF151201=DUF4561=FE(39.2=100),PF0114712=Crust_neurohorm=PU(97.0=95.6)
A:
NA
C2:
PF151201=DUF4561=FE(28.7=100),PF0114712=Crust_neurohorm=PD(1.5=2.0)
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:
TGGACCACCACTGTAACAACT
R:
ATTACACAGCATGCGTCGTGG
Band lengths:
338-724
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]