HsaINT0146236 @ hg38
Intron Retention
Gene
ENSG00000146197 | SCUBE3
Description
signal peptide, CUB domain and EGF like domain containing 3 [Source:HGNC Symbol;Acc:HGNC:13655]
Coordinates
chr6:35240374-35241266:+
Coord C1 exon
chr6:35240374-35240490
Coord A exon
chr6:35240491-35241140
Coord C2 exon
chr6:35241141-35241266
Length
650 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGC
5' ss Score
7.79
3' ss Seq
CTCCCTACTCCTTCCCCCAGATG
3' ss Score
10.94
Exon sequences
Seq C1 exon
ATATAGACGAGTGTTCCTTTGATCGAACCTGTGACCACATATGTGTCAACACACCAGGAAGCTTCCAGTGTCTCTGCCATCGTGGCTACCTGTTGTATGGTATCACCCACTGTGGGG
Seq A exon
GTAAGCTAGTAAGCTTGCACCCCCAGCCACCCTGGCCCCCTCACCTCTTCACCCTCCAATTGAACAGGTCCTTGTGTTGGCTTGTGGCTATGGGCAATCCCTGGATGCATGCACCATGTCTGCATCCGCTGTGACAAAATAGGAGGAATTAAGACAGCTTTTGAAGAACTGGGAGACTGCGGAAACAGCATCCTGCCTCCAAAATTCCTATCTCCCATTCCTATAACTGTCCCTGAACCCCCACTCTCAGCTCCCAAATGACAGTCTCACTGGTTGGGAGGAGTGGAAGGCTTTAAAAAGCTTGTTGGCTTGGCCCCTTCTCGATCATTCCTTTGGGGACAGAGATAATTGGAGGAGGTTTGAGCTCTTCTCAGGCCAGTAGTCATCTTACAGTGCCTAGAATGCCTTTTTAACTTTTTTAAATTGTAAGAATATTTAACAAGAGATCTACCCTCTTAAGTTTTTAAGTGTACACTACAGTATTTATGTGCCTATAGGCACACTGTTGTACAGTAGATCTCTCGAACTTATTCATCTTGCGTAATGCAGGGTACCTGAAACTCTAACCAAAGGCCCTCACTCACTGCCTACTCTCCGGCTCCTCCTCCAACTCCATCGTTGTTTTTCTGTCTCCCTACTCCTTCCCCCAG
Seq C2 exon
ATGTGGATGAATGCAGCATCAACCGGGGAGGTTGCCGCTTTGGCTGCATCAACACTCCTGGCAGCTACCAGTGTACCTGCCCAGCAGGCCAGGGTCGGCTGCACTGGAATGGCAAAGATTGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000146197:ENST00000274938:9
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:
PF0764510=EGF_CA=WD(100=95.0)
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=86.0)
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:
ATATAGACGAGTGTTCCTTTGATCGA
R:
CAATCTTTGCCATTCCAGTGCA
Band lengths:
238-888
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