HsaINT0146220 @ hg19
Intron Retention
Gene
ENSG00000146197 | SCUBE3
Description
signal peptide, CUB domain, EGF-like 3 [Source:HGNC Symbol;Acc:13655]
Coordinates
chr6:35209981-35210557:+
Coord C1 exon
chr6:35209981-35210097
Coord A exon
chr6:35210098-35210398
Coord C2 exon
chr6:35210399-35210557
Length
301 bp
Sequences
Splice sites
5' ss Seq
CAGGTTTGG
5' ss Score
5.63
3' ss Seq
TGACAAGCCCTCTCTCCCAGGTG
3' ss Score
6.46
Exon sequences
Seq C1 exon
AGGCTGCAGTGCTGTCCATTAAACAACGGGCCTCCTTCAAGATCAAGGATGCCAAATGCCGTTTGCACCTGCGAAACAAAGGCAAAACAGAGGAGGCTGGCAGAATCACAGGGCCAG
Seq A exon
GTTTGGACTGGGGACCCCATTCCAGTTGGCTGTCTGGCCACTAAATCCTCCTTACCCCTCAGCTCCTCTGCTTCCAAAAACCCACCAGAACCCTGAACTCTAGGCAGAGCAGAGGAAAAAGCAGCTGTAGGCATAGCACCCAAGGAAGTCCCAGAATATTCCCCTCCACCAACTAATTAGGACCCTAGACTAAAACAGGATTGAGAGATAGTTACAGTTAGAGATCTGGGGAGGTCTGTCTGGGCTGGGAGTGAGAACTTTCCAGGGGATGTCCCTGGGGTTGACAAGCCCTCTCTCCCAG
Seq C2 exon
GTGGTGCCCCCTGCTCTGAATGCCAGGTCACCTTCATCCACCTTAAGTGTGACTCCTCTCGGAAGGGCAAGGGCCGACGGGCCCGGACCCCTCCAGGCAAAGAGGTCACAAGGCTCACCCTGGAACTGGAGGCAGAGGTCAGAGCCGAAGAAACCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000146197-SCUBE3:NM_152753:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.200 A=NA C2=0.444
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GGCTGCAGTGCTGTCCATTAA
R:
GTGGTTTCTTCGGCTCTGACC
Band lengths:
273-574
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)