HsaINT0146222 @ hg38
Intron Retention
Gene
ENSG00000146197 | SCUBE3
Description
signal peptide, CUB domain and EGF like domain containing 3 [Source:HGNC Symbol;Acc:HGNC:13655]
Coordinates
chr6:35243021-35243755:+
Coord C1 exon
chr6:35243021-35243236
Coord A exon
chr6:35243237-35243593
Coord C2 exon
chr6:35243594-35243755
Length
357 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGG
5' ss Score
8.37
3' ss Seq
CGCGGCCGACTCTCCCTCAGTCA
3' ss Score
5.74
Exon sequences
Seq C1 exon
CCAGCTGTGGGCTGCCCTGCCTCCGACAGCGAATGGAACGGCGGCTGAAAGGATCCCTGAAGATGCTCAGAAAGTCCATCAACCAGGACCGCTTCCTGCTGCGCCTGGCAGGCCTTGATTATGAGCTGGCCCACAAGCCGGGCCTGGTAGCCGGGGAGCGAGCAGAGCCGATGGAGTCCTGTAGGCCCGGGCAGCACCGTGCTGGGACCAAGTGTG
Seq A exon
GTAAGGGAGCTTACTGGGGAGCAGGGATGTAGGAAAGACCCAGTTTGGGCCTGACTCAGAGCAGGACCCTTTGTGGCCTCAGATGCATTTCTCAAATTATGAGGCAGCCAGGATGCTCCTGCCCGCTGTCCTCCCTTCCTTGGTTCCAGGCTGAAATCTAGAAGGATGCCAGGTGGGGCCAGCAATCCTCCTGCACACGGTTTTGACCCTCCTATCCCCCCAAGTAGGATTGTGTTTGTTCCCTGACAGAGATTCTCCCTGAATCGGGGGTTGTGGCGGGGAGTGGGAAGGGGAGTCCCAGGCCTGGGTGGTGGGAAATGCGGGGGTGGGTGGCTAGCGCGGCCGACTCTCCCTCAG
Seq C2 exon
TCAGCTGCCCGCAGGGAACGTATTACCACGGCCAGACGGAGCAGTGTGTGCCATGCCCAGCGGGCACCTTCCAGGAGAGAGAAGGGCAGCTCTCCTGCGACCTTTGCCCTGGGAGTGATGCCCACGGGCCTCTTGGAGCCACCAACGTCACCACGTGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000146197:ENST00000274938:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.219 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF076998=GCC2_GCC3=WD(100=87.3)
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:
CCTCCGACAGCGAATGGAAC
R:
GTGGTGACGTTGGTGGCTC
Band lengths:
351-708
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