HsaINT0159560 @ hg19
Intron Retention
Gene
ENSG00000197558 | SSPO
Description
SCO-spondin homolog (Bos taurus) [Source:HGNC Symbol;Acc:21998]
Coordinates
chr7:149521483-149522213:+
Coord C1 exon
chr7:149521483-149521761
Coord A exon
chr7:149521762-149522053
Coord C2 exon
chr7:149522054-149522213
Length
292 bp
Sequences
Splice sites
5' ss Seq
CTGGTAATG
5' ss Score
5.67
3' ss Seq
CTCCATCATACCTTCCCCAGACT
3' ss Score
6.26
Exon sequences
Seq C1 exon
GTCTTCTGCCTCTGAGTGAGTGGTCCGAGTGGTCGCCCTGTGGGCCCTGCCTGCCGCCCAGCGCCCTGGCCCCTGCCTCCAGGACTGCCCTAGAGGAGCACTGGCTCCGAGACCCAACTGGCCTCTCCCCCACCTTGGCCCCGCTGCTGGCTTCAGAGCAGCACCGCCACCGGCTCTGTCTGGATCCTGCGACAGGGAGGCCCTGGACTGGAGCCCCTCACCTCTGCACCGCACCCCTCAGCCAGCAGCGCCTCTGCCCTGACCCTGGAGCCTGCCCTG
Seq A exon
GTAATGGGGAGAGGCAGAGGCCAGGGGACAGGACGGGCCTGGAGTGCAGGTTGGGGGGACCTGGCCGGGAGGGGCTAGGCTATAGAGCACATTGACCTGCTACCCCTCCTGCTTGTCTCTAAGGCCTGCAGGATTTGAAGCTGGGGGTGGGGTCCAGGCAGCAGCTAGAAAGAGAAGCGGGAGAGCCTAGAGGGCTTTAAGGCCTGCCGGAGCGTTTGCGACGACAGAGCTCAAGGCTTGAGGGGGAGGCAAGAGGTGGGCCTGGGTACTGACTCCATCATACCTTCCCCAG
Seq C2 exon
ACTCATGCCAGTGGAGTCTGTGGGGGCCATGGAGCCCCTGCCAGGTGCCCTGCAGTGGGGGGTTCAGGCTACGCTGGAGAGAGGCAGAGGCCCTCTGTGGAGGAGGCTGCCGGGAGCCATGGGCTCAAGACAGAAAGCTGCAACGGAGGGCCCTGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197558-SSPO:NM_198455:90
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.074 A=NA C2=0.355
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGCCTCTGAGTGAGTGGTC
R:
ACAGACTCCACTGGCATGAGT
Band lengths:
296-588
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
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)