HsaINT0156587 @ hg19
Intron Retention
Gene
ENSG00000165643 | SOHLH1
Description
spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Source:HGNC Symbol;Acc:27845]
Coordinates
chr9:138586896-138588651:-
Coord C1 exon
chr9:138588458-138588651
Coord A exon
chr9:138587110-138588457
Coord C2 exon
chr9:138586896-138587109
Length
1348 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
GCATCTGACTTCTCTCCCAGAAC
3' ss Score
7.93
Exon sequences
Seq C1 exon
AACCCCAGATGTGAAGGCGTTTCTGGAAAGTCCTTGGTCCCTGGATCCAGCGTCGGCCAGCCCAGAGCCCGTGCCGCACATCCTTGCGTCCTCCAGGCAGTGGGACCCCGCGAGCTGCACGTCCCTGGGCACGGACAAGTGTGAGGCACTGTTGGGGCTGTGCCAGGTGCGGGGTGGGCTGCCCCCTTTCTCAG
Seq A exon
GTGAGTCCTGGGTGTGCATGTGGGGTGCCTTTGGCCTGGGGAGCGGCGCCAGGCTGTGCTTTAGCCCTAAGAACAATGGGGGCTGTTTGCAAACGGGGTTCGAAGTTTTCCCAGGCCCTTGTGTTGGTGAGAAACCCACGTGTTGAGGGATGAGCTTGATTCAAGGCCCCCGGGCTGTGCCTGCTTTTGTGAAAAGGAGGACGTGTGCTCTCGGGAGGGAGGAAGTGTGGCTCGAGGAAGGGAGAGTCCTGGGCAAAGGCCACCATGGGAGCTGTTCCTTCTATCCTGTCTCCTCCTGGGACTTCCATGTGCTCCAGGGAAGGGAGGGCCTGATCTTCTCCTCCCTGGGTCCCTGGGTCTGCTGGGAAGCATGGGGACGTAGAGGGACTTGGCCCCATCCTGGTCACTCCCTGGGTCTGCAGGAAGTATGGGGACGTAGAGGGACTTGCCCCATCCTGGTCACTCCCTGGGTCTGCTGGGAAGCATGGGGACGTAGAGGGACTTGGTTCTGTCCTGGGTCTGTGGGAAGTGGGGAGGTAGAGGGACTCGGCCCCATCCTGGTTGCTCCGTCCAGCTTTGTGGCCCTGCTTCTCTCACCCGCCTGTGGCTGGTGTGTTTTGGATGTGGCCGGAGATCTGTTTTCCCCGGGGCGCCCCATCTGCCCTTCCGCCTATGCTGCCTGGCCATGGCAGGAACTGTAATTGGGGTGAGCCAGGGGCCCGAGGCCTCCCAGCTGTTCCCTCTGCCACCCGGGGCCTTTGTCCCTAATGCCACCCACAGCTGAGCTCTGGTCCCTCTGTGGGTGGCCCTGCAGGGCGCCTCTGATGACCGAACTCCCCTCGGCCCCTGCTGTGGTAGCGTCTGGAAGTCGCCAGGTGCCATGAGAGGCAGGGCTGTGCCTTTTGGCTCCCAGCTGTGGCTGGGAGCAGTCATGCAGTTGGCAGGGCTGGTGTCAGAGCTGGGGTCATCAGGGCACTCCGGAAACCCAGGAGTCAGCCAGGCACGTGGGGAGCGAGCAGGTCTGAGGGCAGAGCTCGAGGTCCGGGAGGCGGTGCTGAGAGGGTCCCCAGATCCAAGCCCCTTGCGGCTGGCCAAGCCAGCACCCCCTCTAGGAAGCCCTTGGCCCCCAGGTGTTGGGCACCCCACCTCTGGGTGTTCATCTTTTCCTTGTTTACCTGTGTGCCACCCGCTTCTGAGCTTCCTCCCACGTGTCCCTGCTGCAGGGTGCAGGCAGCAGAGCAGGTGCTCGGTCAGTGTGAGTGGACCGAGCCCGTGAGTCACGAGGTCCTCGGGGGCAGCCTGTGGGGCTGGGCAGGGAAGGCTGACCCGCATCTGACTTCTCTCCCAG
Seq C2 exon
AACCTTCCAGCCTGGTGCCGTGGCCCCCAGGCCGGAGTCTTCCTAAGGCTGTGAGGCCACCCCTGTCCTGGCCTCCGTTCTCGCAGCAGCAGACCTTGCCCGTGATGAGCGGGGAGGCCCTTGGCTGGCTGGGCCAGGCTGGGCCCCTGGCCATGGGGGCTGCACCTCTGGGGGAGCCAGCCAAGGAGGACCCCATGCTGGCGCAGGAGGCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165643-SOHLH1:NM_001101677:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.455 A=NA C2=0.843
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGTCCTTGGTCCCTGGATCC
R:
TCCTCCTTGGCTGGCTCC
Band lengths:
357-1705
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)