HsaINT0156583 @ hg38
Intron Retention
Gene
ENSG00000165643 | SOHLH1
Description
spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Source:HGNC Symbol;Acc:HGNC:27845]
Coordinates
chr9:135698995-135699528:-
Coord C1 exon
chr9:135699403-135699528
Coord A exon
chr9:135699127-135699402
Coord C2 exon
chr9:135698995-135699126
Length
276 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGG
5' ss Score
5.85
3' ss Seq
GCTCTTGGCTTTCTCGGCAGCGG
3' ss Score
6.86
Exon sequences
Seq C1 exon
GGGGGCGGGGCTGCCTGCGGAAGGGGCCGTGCGCGTGGGGTCGCTCCGCAGCTGCGAGTTCATGGCGTCCCGGTGCTCCGAGCCCTACCCGGAGGTCTCCAGAATCCCTACCGTCAGGGGATGCAA
Seq A exon
GTGAGGAATTGGGCTGGCGGCCAAGGGGTTGGGGGCCCAAGGCCTGTACCCAGGGGTTCTTCCGCAAGTTGCTGGGCTCCACCCATCCTGGGCCTCCTGGGGCGGAGCCCTGGACCCTGGGAGAGGGGAAGGGGTGCAGAGAGGGCCGGGCCGTGTCCCTACGTGACCCAGTCTTGGCTTCCACCCGCACCCCAAAGACGCCCATTCTGGCATCTGGGACTCCTGGTGGCCTTTTCTGGGGTTCTCAGGGCCCGGTGCTCTTGGCTTTCTCGGCAG
Seq C2 exon
CGGCTCCCTGTCTGGTGCCCTCTCCTGCTGCGAGGACTCGGCCCGGGGCTCGGGCCCGCCCAAGGCCCCTACGGTGGCCGAGGGTCCCAGCTCCTGCCTTCGGCGGAACGTGATCAGCGAGAGGGAGCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165643:ENST00000298466:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.489
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0001021=HLH=PU(20.8=22.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
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:
CAGCTGCGAGTTCATGGCG
R:
TCCCTCTCGCTGATCACGTTC
Band lengths:
204-480
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains