BtaINT0139001 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006558 | SOHLH1
Description
spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Source:HGNC Symbol;Acc:HGNC:27845]
Coordinates
chr11:103350309-103350967:-
Coord C1 exon
chr11:103350879-103350967
Coord A exon
chr11:103350457-103350878
Coord C2 exon
chr11:103350309-103350456
Length
422 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGG
5' ss Score
6.92
3' ss Seq
GGTCCCTTCTCTGCGAGCAGGAA
3' ss Score
5.56
Exon sequences
Seq C1 exon
CAGGGTTCGGGCCAGACCAAGGGGCCTGCGGTGGCGGAGGGTCCCGGCTCCCACCTGCCACGGAACGTGCTCAGCGAGAGGGAGCGCAG
Seq A exon
GTGGGGGCCGTCGTGGCGGCCGCGCGGTGGGGGCGGGGGTCCGAGGAGGTCAGGTCTGCGCCCGCCGCCTAGTTTCAGACAGCTGTTTGGTAAGGGCACGCTGTAGCGAGTTCTCAAGGTAAATATAGCCCTCGTGCTGGGGGAGGGCCACCAGTGCAGCCCTTTCTTTGACGTGAAGTTCAGGGCCACTCGAGGTTGTACGTTTGGGGCTGGTCCCCGCTCCAGGCAGGGGTGGTGGTCTAGGCTTGGTGGTGGCCTGTGGCAGACGCCCTGCTAAGCCTGCAGCTGGGGTCCAGGGCCCCTGGGGCCAGGGCAGTGCTCTGACCTGGTTCCTGAAGGGCTCAAGGCTTTCTGGGGCTGTCCTCTCGTTTCCTGGCCAAGCCAGACAACCCTACAGTCGGGGGTCCCTTCTCTGCGAGCAG
Seq C2 exon
GAAGCGGATCTCCTTGAGCTGTGAGCACCTGCGGGGTCTGCTGCCGCGGTTTGACGGCCGGCGGGAGGACATGGCCTCGGTCCTGGAGATGGCAGTGCAGTTCCTCCAGCTGGCAGGCACCCTGGTGCCCGGCTGGGAGCAGCAGGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006558:ENSBTAT00000008615:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.867 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0001021=HLH=PU(19.1=30.0)
A:
NA
C2:
PF0001021=HLH=PD(78.7=74.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
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:
CAGGGTTCGGGCCAGACC
R:
CCTGCCAGCTGGAGGAACTG
Band lengths:
206-628
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development