BtaINT0139003 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006558 | SOHLH1
Description
spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Source:HGNC Symbol;Acc:HGNC:27845]
Coordinates
chr11:103349492-103349850:-
Coord C1 exon
chr11:103349732-103349850
Coord A exon
chr11:103349604-103349731
Coord C2 exon
chr11:103349492-103349603
Length
128 bp
Sequences
Splice sites
5' ss Seq
GATGTCAGT
5' ss Score
1.36
3' ss Seq
GCTGTGAGGCTGCGGCTGTGGAC
3' ss Score
-18.67
Exon sequences
Seq C1 exon
GCTCTCACTTCCTCCAAGGAGCCGTGGCTCGCATGGCAGACGGATGTCCTGCAGCTGGCCCTGGCGAGTCAGGCCCCGGCAGGCGCCCCGGACGCCGGCGTAGGAACATCCAGTGTGAT
Seq A exon
GTCAGTGTCCCCGTGGGGCCGGGGGCCATGGTGGGGGGGGGTGCGTGCAGACCACTCAGAGGCTCTCTTTTTGTCTTTGCACACCATGCAGTCATCAGGCCCCCCCGAGCTGTGAGGCTGCGGCTGTG
Seq C2 exon
GACGAGGGTGAGGCCCTTTATGGGGGTGGCCGACATGCTGGACAGGCCACCAGCGCTGCCTAGTGAGTGTGAGTGGGTCCCCGTCCTCCCCTCATGCTGTCCACAGCCAGGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006558:ENSBTAT00000008615:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.325 A=NA C2=0.053
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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:
GCTCTCACTTCCTCCAAGGA
R:
CTGTGGACAGCATGAGGGGAG
Band lengths:
225-353
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development