HsaINT0159475 @ hg19
Intron Retention
Gene
ENSG00000197558 | SSPO
Description
SCO-spondin homolog (Bos taurus) [Source:HGNC Symbol;Acc:21998]
Coordinates
chr7:149479270-149480110:+
Coord C1 exon
chr7:149479270-149479387
Coord A exon
chr7:149479388-149479934
Coord C2 exon
chr7:149479935-149480110
Length
547 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGCC
5' ss Score
7.13
3' ss Seq
CATCAGACCCCCTGTTCCAGGAG
3' ss Score
5.11
Exon sequences
Seq C1 exon
GACTATGTGAAGGGACAGCTACTGATCCTACTGGAGCATGGGGCCTGCGACGCTGGGAGCTGCCTGCACGCCATCTCCGTCTCCCTGGAGGACACCCACATCCAGCTCAGGGACTCAG
Seq A exon
GTAGCCTCTGCTCTGCACTCTTGAGGCAGTCTCAGGCCTCCTGTCACTGCTCCTCCTCCACACTACCCTATGGCTTTGGAGTCCAAACACTCTTCCCCAGCCTCCTACACCTAAGCACACTGCCTCAACTTCCCCGGCCCTCTCATCTCTGAAGCAGACATACAGAGTCCTGAGGAGATGTTCCGAGGCATCTTCTGCCCCGTCCTGGGGTCAGATACAAGTCATGCAGCTATGAGAGCTTGAAAGGCCTTAAGGCATGACCAGACCGGGCAGGCCACTCAGCAGGGTCCCTCCAACCCTCCCCAACCAGCTCCTGGCTTGCCATCTAGCTCCTCCCACACACTGATCATGAGGGTGAGGGACTGGAAAATCTGTGTGCCAAGGGTAGTCCTTGGGCCGCAGGGGTAGGGAGCTCAGGTGGACACTCTAGTTGTCCCCAGCAGCCCATCCTGACATGGGACTTTCTACTTCCCATCCAAGCTCCTTCCCTTATCGCAGCCCTATCCTTCCACGTGCCCCACCCCCACCATCAGACCCCCTGTTCCAG
Seq C2 exon
GAGCTGTGCTGGTCAATGGGCAGGATGTGGGCTTGCCCTGGATTGGCGCTGAGGGCCTCAGTGTGCGCCGAGCTTCCTCTGCCTTTCTGCTGCTGCGCTGGCCTGGGGCCCAGGTGCTCTGGGGACTGTCTGACCCTGTAGCCTACATCACCCTGGACCCCCGCCATGCCCACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197558-SSPO:NM_198455:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.140 A=NA C2=0.000
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
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTATGTGAAGGGACAGCTACTGA
R:
GGGGTCCAGGGTGATGTAGG
Band lengths:
278-825
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)