GgaINT0016667 @ galGal4
Intron Retention
Gene
ENSGALG00000003377 | SIMC1
Description
SUMO-interacting motifs containing 1 [Source:HGNC Symbol;Acc:HGNC:24779]
Coordinates
chr13:9756609-9757146:-
Coord C1 exon
chr13:9757054-9757146
Coord A exon
chr13:9756830-9757053
Coord C2 exon
chr13:9756609-9756829
Length
224 bp
Sequences
Splice sites
5' ss Seq
GGGTTCAGA
5' ss Score
-7.78
3' ss Seq
CTGCCTTACCTTGCACACAGCGG
3' ss Score
7.52
Exon sequences
Seq C1 exon
CTAAACAAACTGCGCTATTTCAGGAGGAGTGGAGTCCAGCACCTCTTCTTTCATGGTGCAACATCTGACAGGGAAACACCACAGGTAAATGGG
Seq A exon
TTCAGAGCAGCTACTGCCCAGCCAGGTCCACTCAGAGCAGTTCTTGTGGCAGAGGATGGAGCACGGGCTGCCCCCTGCTCCACTTCCCCTTTCAGGGGAAGCTTTGCCAAGCCATTGGGATCTCTGGTTACTGCAGTTCTCTTAATGGTGGGCCTCAAATCACAGCTAGATCCCCGTGTACCATGGGGACCCAGTTTTCACCCACTGCCTTACCTTGCACACAG
Seq C2 exon
CGGAAACCCGAGCTCATCCCCAGCAGTAAGATGAGCATGGTACGCACCACCATGGAGGAGAACTTCCTGGAGGGAACCTTGCATTTCCTCAGTGACTTCATCTCCCGCCAGCACTGCCCTCCCAAAGAAATCGTCTCCCATCTGATCAGACACATCCTGTTGAACTCCCACCAGGAGGAGATCCTCCAGAACACCTACACGCTGCTGATGAAGATCCAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003377:ENSGALT00000005337:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.323 A=NA C2=0.135
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGCTATTTCAGGAGGAGTGG
R:
GGATCTTCATCAGCAGCGTGT
Band lengths:
299-523
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]