BtaINT0139005 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006558 | SOHLH1
Description
spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Source:HGNC Symbol;Acc:HGNC:27845]
Coordinates
chr11:103346206-103347183:-
Coord C1 exon
chr11:103347113-103347183
Coord A exon
chr11:103346518-103347112
Coord C2 exon
chr11:103346206-103346517
Length
595 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
CACGTCCCATCTGCTTCCAGGGT
3' ss Score
9.94
Exon sequences
Seq C1 exon
GTCTGTGTCGGGATGTGACGTGGCAGATGGTGCGTCTGTTCTGCTGAGCCCTGGGCCTGACTGGTGGTTGG
Seq A exon
GTGAGTGGACCGCTTTCCTACCACCCCCAACCTGGAGCCTGGGTTGGTCCTCAGGCAGGGCTGGGGGCAGGCAGCTGGGACCGTGGGGAGATGGGCCCCAGCTTGCCGAGTGACGCCAAGCTTCCAGTGTCTGCATCTGAGTTCTCGTTCCCTTCTCTGCTGGTGTTTTTGGGGACCCCTGGGTCGGTGGGGGGGATGGCAGGTGAGGTGCATGCTGATCGGCGGTGGGCATCTGTGGGTGAGAGTGTGTGAGTGCTGGGTGTCGGTGGCTGCAAGTCGGCTTCAGAGCTTTCCCCCAAGAACTCGTGCCCACAGAGGCACGTGGGTGCGGGGTGAGTCGAGCGTGTGCAGGATCTGGCGTGGAGGGGGTGCACCTCCCTGGTTCTGGCCCTCCCAGGGGTCTTGAGCAGGGCCAGCAGGAGTGGGCCCACCCACCTGGTCAGGGGCCCTTCTGAGGATGAGCAGGGGACTTCTTGGTGGGGTGGGACAGATGGGTGGGGGGAAGGGTGTCATCTTCTCTACGCTGACCCTACCCTGCCCACCATGGGTCCTGGGGTCCTTGTCTGCTCTGCTGACACGTCCCATCTGCTTCCAG
Seq C2 exon
GGTCCCTGGAGGGCAGAGGCAGCGGCGCCCCTTCTCGGGTAGCCACCAGGAACAGCCCGCTGGACAGGCTCGAGCCGGGCTTCCTGGGAGACCCCGAGTCTGGCCCCCAGGAGGAGTCCCCGGACGGGCCCCTGGAGCCGTGGGGCTCGGATGGGAGCTGCTCCAGCCCAGTCCTGCGGGATGAGGTGGACAGCATCTTCCCCGACTTCTTCGCCTGCTGAGACCAGGGGAACGGGACCTTTTCGGCAGCACGTGCCACACACTCGGGCGGGGTTTTATTCTGGGTTTGGGCTGCAGCTGTGGTCTAATTCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006558:ENSBTAT00000008615:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.200 A=NA C2=0.767
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
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:
GATGTGACGTGGCAGATGGTG
R:
AACCCAGAATAAAACCCCGCC
Band lengths:
347-942
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development