BtaINT0008184 @ bosTau6
Intron Retention
Description
Bos taurus carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 6 (CHST6), mRNA. [Source:RefSeq mRNA;Acc:NM_001192022]
Coordinates
chr18:2866949-2869038:-
Coord C1 exon
chr18:2868963-2869038
Coord A exon
chr18:2868153-2868962
Coord C2 exon
chr18:2866949-2868152
Length
810 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGT
5' ss Score
9.07
3' ss Seq
ACTGCCTGCTCCCTCTGCAGGTC
3' ss Score
12.77
Exon sequences
Seq C1 exon
GCCCTGAAAAACCTCCAGGCCTCTCCCATGGACCTGTGATCGAGGTGGGCAGCCCTCCCAGCAGCCAGGGACAGCA
Seq A exon
GTAAGTAACCTTAGCATGGAAAGGGGCCCGACTCTGCCCTCATCTTTCCCCTTCTCCGGCTCCGTCCTACCTCTCCCTTAACTGGTTTCTTCTGCCAAACCCCACCAATCCAGAAGGATATCCTCCCTTGGGAATCCGTGCTTCCTGCAGGACTTCACTCTCCATGGGTGAGAGCAACAGTTGCTGTTTTTTGTCTATTTATTTGTAATAGCAAAAGTAACATCTGCTTATTTAAAAAGTCAAACAATACAGAAGCACACTAGGCAGAAAGTGCAAGTTTTCAGTTATGAGAATTACTACATGCCCCAACCCTCGGGACTCATCCCAATACTCCAGGACCAAGATGAATCCCCTTTTACAGATGGGTGAACTGAGTCACAGAGCAATGAAGCCTTTGGTCTGAGATGTTAGGCTAGGAAGTGGCGCAGTTGGGAAGGCTCTGCTAAATCATCCAGCAAGCTATTTAGGTAAACAACCTAAAATTGCTCCCCTATAAGGAATTTTAAGCAAAAAGCAGGACTTCCGGTTTACATATATGTTCCCCCTGAGAAAGAAAAGGGCTAGGGGAGAGAAAGAGAGACAAAGGGAAGAACATTGCCCATAGTCTTGTGCAGCTGGCGTTTGGCTCTGCAAAGACTGCTCATGCCTTCAAGTCACACTCCTGACTTGGGAGGTCCTCAGTGGGGTGATCTCCCTGGGGCGGTGGGCAAGTTCCAGAGCTGCTCTCCGGCAGCCCCAGACCGGGATGTGGGATGTGGGATGGGCAAGTGGCCCCTGATCCCCGACTGCTACTGCCTGCTCCCTCTGCAG
Seq C2 exon
GTCTCCGGCCGGCGGCATGTGGCTGCGGCGCGTCTCCAGCACGGCGGTGACTGCGCTCCTGCTGGCGCAGACCGGCCTCCTGCTCTTCCTGATCTCCCGGCCCAGACTGCCGCCTGCGGCCAGCAGCGAGGAGCGGGTGCATGTGCTAGTGCTGTCCTCGTGGCGCTCGGGCTCGTCCTTCGTGGGCCAGCTCTTCAGCCAGCACCCCGATGTCTTCTACCTGATGGAGCCCGCGTGGCACGTGTGGGCCGCCCTGTCGCAGGGCAGCGCCTTGGCGCTGCACATGGCAGTGCGCGACCTGGTGCGCTCAGTCTTCCTGTGCGACATGGATGTGTTCGAGGCCTACCTGCCGTGGAGGCGCAACCTGTCGGACCTCTTCCAATGGGCGGAGAGCCGGGCTCTGTGCTCGCCGCCCGCCTGCAGCGCCTTCCCGCGCGGCGCCATCAGCAGCGAGGCGGTGTGCAAGCCGCTGTGCGCGCGGCGGCCCTTCAGCCTGGCGCAGGAGGCCTGCCGCTCCTACAGCCACGTGGTGCTCAAGGAGGTGCGTTTCTTCAACCTGCAGGTGCTCTACCCGCTGCTCAGCGACCCAGCACTCCACCTGCGCATCGTGCACCTGGTGCGTGACCCGCGCGCTGTGCTGCGCTCGCGCGAGCAGACGGCCAAGGCGCTGGCGCGCGACAACGGCATCGTGCTGGGCACCAACGGCAAGTGGGTGGAGGCCGACCCGGAGCTGCGCGTCGTGCGTGAGGTGTGCCGCAGCCACGTGCGCATCGCCGAGGCGGCCACGCGCAAGCCTCCGCCAGCCCTGCGCGGCCGCTACCGCCTGGTGCGCTTTGAGGATCTGGCGCGGGCGCCGCTGCCGGAGATCCGAGAGCTGTACGCCTTCGCGGGCCTGAGCCTCACGCCGCAGCTCGAGGCCTGGATCCACAACATCACGCACGGCGCCGGGCCCGGGGCGCGCCGTGAGGCCTTCAAGACCACGTCAAGGGACGCGCTCAATGTCTCACAGGCTTGGCGCCACGCCCTGCCCTTCGCCAAGATCCGCCGCGTGCAGGATCTGTGTGCCGGAGCACTGCAGCTGCTGGGCTACCGGCCAGTGTTCTCCGAGGACGAGCAGCGCGACCTCAGCCTGGACCTGGTGCTGCCGCGCGGCCCCAGCAGCTTCAGCTGGGCCTCGTCCACTGCTGAGCGCCCCGGGCCGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000040000:ENSBTAT00000056191:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0068522=Sulfotransfer_1=WD(100=80.3)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion 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:
CCTCTCCCATGGACCTGTGAT
R:
CCATGTGCAGCGCCAAGG
Band lengths:
344-1154
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development