HsaINT0156583 @ hg19
Intron Retention
Gene
ENSG00000165643 | SOHLH1
Description
spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Source:HGNC Symbol;Acc:27845]
Coordinates
chr9:138590841-138591374:-
Coord C1 exon
chr9:138591249-138591374
Coord A exon
chr9:138590973-138591248
Coord C2 exon
chr9:138590841-138590972
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-SOHLH1:NM_001101677:1
Average complexity
IR-S
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
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
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)