HsaINT0146223 @ hg38
Intron Retention
Gene
ENSG00000146197 | SCUBE3
Description
signal peptide, CUB domain and EGF like domain containing 3 [Source:HGNC Symbol;Acc:HGNC:13655]
Coordinates
chr6:35243594-35244130:+
Coord C1 exon
chr6:35243594-35243755
Coord A exon
chr6:35243756-35243962
Coord C2 exon
chr6:35243963-35244130
Length
207 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCCA
5' ss Score
3.75
3' ss Seq
GGGCCCTTGATTCATTGCAGGTC
3' ss Score
7.57
Exon sequences
Seq C1 exon
TCAGCTGCCCGCAGGGAACGTATTACCACGGCCAGACGGAGCAGTGTGTGCCATGCCCAGCGGGCACCTTCCAGGAGAGAGAAGGGCAGCTCTCCTGCGACCTTTGCCCTGGGAGTGATGCCCACGGGCCTCTTGGAGCCACCAACGTCACCACGTGTGCAG
Seq A exon
GTGCCAGGGGAACAAACAATACAGAGTGGGGTAGGGTGGGCACTGGGATGCCCATGGGCATGGGATTTCCCAAAGGGCAGGCCCAGGCTCCAGGCCACTCTCTTAGTCAACATCCTGTTTGTATACCTTTGTCCCCTGAGATCGGGTGACCCCATGGGGATGACTCAGGACCATCCCCATCAGAGTTGGGCCCTTGATTCATTGCAG
Seq C2 exon
GTCAGTGCCCACCTGGCCAACACTCTGTAGATGGGTTCAAGCCCTGTCAGCCATGCCCACGTGGCACCTACCAACCTGAAGCAGGACGGACCCTATGCTTCCCTTGTGGTGGGGGCCTCACCACCAAGCATGAAGGGGCCATTTCCTTCCAAGACTGTGACACCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000146197:ENST00000274938:16
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:
PF076998=GCC2_GCC3=WD(100=87.3)
A:
NA
C2:
PF076998=GCC2_GCC3=WD(100=84.2)
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:
GGAACGTATTACCACGGCCAG
R:
GTCTTGGAAGGAAATGGCCCC
Band lengths:
303-510
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development