HsaINT0156585 @ hg19
Intron Retention
Gene
ENSG00000165643 | SOHLH1
Description
spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Source:HGNC Symbol;Acc:27845]
Coordinates
chr9:138589352-138590322:-
Coord C1 exon
chr9:138590175-138590322
Coord A exon
chr9:138589474-138590174
Coord C2 exon
chr9:138589352-138589473
Length
701 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
CATGTTTACTTAAATTTCAGATT
3' ss Score
8.71
Exon sequences
Seq C1 exon
GAAGCGGATGTCGTTGAGCTGTGAGCGTCTGCGGGCCCTGCTGCCCCAGTTCGATGGCCGGCGGGAGGACATGGCCTCGGTCCTGGAGATGTCTGTGCAGTTCCTGCGGCTTGCCAGCGCCCTGGGGCCCAGTCAGGAGCAGCACGCT
Seq A exon
GTGAGTTGTAAGGGTAGACGCCGTCAGTCCTCCGGCATCACGGTGATGGGACATCTCACCACCTTGCAGGCAGTGTGTCCCCTGTCATCCCCGTCTCCTTCAGCCCTCTGGGTCTCCACGGCTAGAGCAGGCCACGTTTTCGGCAGGGCACTTCCTGATTTGTTCAAGCCTTACCTGTTGTTATTCTGTTCCTGGAAAGGAGCAAGCCTTCCTTTCCAGCCCTCCTGTGCCCCTGAGTCCTGTTCATTGATGGGTTGCCGAGATGCTCCGTGCCAATTTGGGGGAGAGTTGGGGTCTCCTGATCCTCCCTGGCTGAGCACCCCCTAGATCATTTCTCTGCACGTCTCCAAGAGAGAGGCTCCTCTCCCCTCTCCAAGGCTCTGGGGGCTCTGGCTGACCCCGTGAGTGCTGGGGCTGAGGACCTGTGTGGGGAATGAAACTGTGTTGTCATCTGTGAGGTCAGGGGTCCCAGCATTTGCAGTGAGGCCCTTGGGTATGCACAGCCTGATTCAGGAATGGTGGGGCCTTTCGGGGGTGGAACCTCAGCCTCGTTGTCAACCTGTACTCTCGCCCCCAAGTTCCAAGCGGGGACCGAGCTCACAGTGACCCTCCAGGCCCTGGGGTAGCAGTCTTGTCACCGTGTCTTGGGTTTCTCAGCTGACTGTCTCTGTCTTTGTTTTACATGTTTACTTAAATTTCAG
Seq C2 exon
ATTCTTGCTTCCTCCAAGGAAATGTGGCACTCGTTGCAGGAGGATGTTTTACAGTTGACGTTGTCGAGTCAGATTCAAGCAGGTGTGCCAGACCCTGGGACGGGAGCGTCCAGCGGGACTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165643-SOHLH1:NM_001101677:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.537
Domain overlap (PFAM):
C1:
PF0001021=HLH=PD(77.1=74.0)
A:
NA
C2:
NO
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:
GAAGCGGATGTCGTTGAGCTG
R:
CCAGGGTCTGGCACACCT
Band lengths:
246-947
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)