HsaINT0146226 @ hg19
Intron Retention
Gene
ENSG00000146197 | SCUBE3
Description
signal peptide, CUB domain, EGF-like 3 [Source:HGNC Symbol;Acc:13655]
Coordinates
chr6:35213005-35213873:+
Coord C1 exon
chr6:35213005-35213202
Coord A exon
chr6:35213203-35213720
Coord C2 exon
chr6:35213721-35213873
Length
518 bp
Sequences
Splice sites
5' ss Seq
ACTGTGGGT
5' ss Score
1.96
3' ss Seq
CCTGCTGCTTGCCTTCCCAGCAT
3' ss Score
7.61
Exon sequences
Seq C1 exon
ATCGTCAGTGTGGTGGGGAGCTGGGTGAGTTCACTGGCTATATTGAGTCCCCCAACTACCCGGGCAACTACCCAGCTGGTGTGGAGTGCATCTGGAACATCAACCCCCCACCCAAGCGCAAGATCCTTATCGTGGTACCAGAGATCTTCCTGCCATCTGAGGATGAGTGTGGGGACGTCCTCGTCATGAGAAAGAACT
Seq A exon
GTGGGTGGCTTGCAGAGCTGGGCCAGGGAAGGGCAGTCCAAATCTGGTTAAGGCGGAGAACAAAGAGAGAGACTGATACAGGAAGAAATGGGGCAGTGAAGTTAGGGATCTATGAGGGTGAAATAGTGAGAGGCCTTTAGGAAGAGAGAAGCTAACAAAGGAAAACAGCAATGACACATGTTTGGTAGAAAACAGAGTTAAGAAAGCTAGCAGTGGGGCTAGAACTCCAATGGCGTTACATGTATCACTTTCCTATCCTAGCATTTTTGCCATTCCATTCATTTAAATGTCATATTTATTACACTATGTGAGTGCCCAGGTATCAAGGAGGAATTGTGGAATGAGCCCAGTGGGCAATGGGAGAGGGTGTGGGGTAGGGTGTGTGTATGCGAAGGGGGAGCCTTTGTCAGAATGATTCTCTTGCCCTATACCCCCACCACCAGCTGTACAGCCCACGTTCTAGGAGGGCTTGGGTAGCCTGCCCTGCTGCTCTACTGACCTGCTGCTTGCCTTCCCAG
Seq C2 exon
CATCCCCATCCTCCATTACCACTTATGAGACCTGCCAGACCTACGAGCGTCCCATTGCCTTCACTGCCCGTTCCAGGAAGCTCTGGATCAACTTCAAGACAAGCGAGGCCAACAGCGCCCGTGGCTTCCAGATTCCCTATGTTACCTATGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000146197-SCUBE3:NM_152753:19
Average complexity
IR-S
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:
PF0043115=CUB=PU(57.3=94.0)
A:
NA
C2:
PF0043115=CUB=PD(41.8=88.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCGTCAGTGTGGTGGGGAG
R:
GGTAACATAGGGAATCTGGAAGCC
Band lengths:
344-862
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)