HsaINT0146173 @ hg19
Intron Retention
Gene
ENSG00000159307 | SCUBE1
Description
signal peptide, CUB domain, EGF-like 1 [Source:HGNC Symbol;Acc:13441]
Coordinates
chr22:43617179-43618748:-
Coord C1 exon
chr22:43618644-43618748
Coord A exon
chr22:43617296-43618643
Coord C2 exon
chr22:43617179-43617295
Length
1348 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACC
5' ss Score
8.66
3' ss Seq
GGAATTTTGGCTTTCCCCAGATG
3' ss Score
7.12
Exon sequences
Seq C1 exon
ACTCGGAAAATAGCTACGTCCTGAGCTGCGGAGTTCCAGGGCCGCAGGGCAAGGCGCTGCAGAAACGCAACGGCACCAGCTCTGGCCTCGGGCCCAGCTGCTCAG
Seq A exon
GTAACCCCCCCGGCCTGTCCATGCTGCATGCCACTGGGTGACTTGACTGCATCCAGCAACATGCTGGCGGGGGAGGAAAGGGCACCGCCCAGGGAAGACCTTCCTGCTCTCGGCCCTGCTCCGTGTGGCCTGGGGTGCTGGCGATGAGCCAGGCCCAGGACCTAGAAGCCAGCAGGCTGCAGGCCGAGTTCTAGCCCAGGGTCAGGGGACCGTGGGAGGGCCCTTCCGGCTCTGAGGTCACAGCCAGAGTGGTTCAGGGACTCTAACGTGCTGTGAGTGCACAGATCTCAGACTGTATGGGTGGAGCAAGCCACATCTGCTGTGGCTATTAGGTTCTCCCGAGTCAGAGCTGGCCTGGCCGTGCAGAGCATGCCAAGAAGCGCCGAGGTGCAGCACAGTCCCAGCCCTTTGGGAGTGACCCGCTGGGCTTGGTCGGCATGGCACAGCCAGCCTTAGCTCCTGCCAGCTAAGGAGCTGAGGGTTGTGTCTTCAGCAGCTTTTCTTATTCAGGATGCTGGATTTGATAGATAGGTGCATTTCTGTATGTTTCTTTATTATTATTATTATTATTTTTAAAACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCGTGATCTCGGCTCACTGCAACCTCCGCCTCCCAGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGTGCCCATCACCACACCTGGCTAATTTTTGTATTTTTAGTAGAGACATGGTTTCACCATGTTGGTCAGGCTAGTCTGGAACTCCTGACCTCAAGTGATCCGCCTGCCTCGGCCTCCCAGAGTGCTAGGATTACAGGCGTGAGCCACCGCACCCTGCCCATTTCTATATATTTAATGCATATGTGATTTGATTCTAAGCACCTGTGGTGGTAGGATTCTTTAGTCCAAGGGCTATGATTTGCTCTTGCAAGGAACCGGCAGTCCTGGATCTATAGTATTTCAAAGCCCCTTCCCTTCCTTGCTGTCCTATCTCTCTTCTGTTCTACGCTCTTTCCTAAAGCACAATCATGGCTTGCTGATGGGGAGGAGGTAGGAGGATCCCTGTCCTCCTTCTCAGAAGACCTCTGGCGGGTGGCCCCTGGGCTTGAGCTTGACCCCACCATCCATGTGTTCACCTGTTTTAGGCCTTGCAGGGAGAGAAATGGGGCAGGAGAGGGTCCCCCACCCCAGGAGAGCTGTCGGGGCACAGGGACTCAGATCAAGCCCCACCCCCAGCTCCAGATGGATTTGTCCCCTGGCAGCCCCCGTCCCCCACCACCTCCTTGCCTGCAGGAGAGGCCACCACCTGGGGGAATTTTGGCTTTCCCCAG
Seq C2 exon
ATGCCCCCACCACCCCCATCAAACAGAAGGCCCGCTTCAAGATCCGAGATGCCAAGTGCCACCTCCGGCCCCACAGCCAGGCACGAGCAAAGGAGACCGCCAGGCAGCCGCTGCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000159307-SCUBE1:NM_173050:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.444 A=NA C2=0.358
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
ACTCGGAAAATAGCTACGTCCTG
R:
CTGGCGGTCTCCTTTGCTC
Band lengths:
208-1556
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)