BtaINT0131523 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020959 | SET
Description
Bos taurus SET nuclear oncogene (SET), mRNA. [Source:RefSeq mRNA;Acc:NM_001038564]
Coordinates
chr11:99224369-99225222:+
Coord C1 exon
chr11:99224369-99224482
Coord A exon
chr11:99224483-99225051
Coord C2 exon
chr11:99225052-99225222
Length
569 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTT
5' ss Score
7.64
3' ss Seq
GTTCTTCTGTCTTCATTTAGGAT
3' ss Score
11.86
Exon sequences
Seq C1 exon
TATTTTGATGAAAACCCTTACTTCGAAAATAAAATTCTCTCCAAAGAATTTCATCTGAATGAGAGTGGTGATCCATCTTCAAAGTCCACTGAAATCAAATGGAAATCTGGAAAG
Seq A exon
GTATTTGAGGACTTGGGCATTAATATTTTGTATGGTTTGATTTAGTTGAACCATTTTACTAATACTTGGTATTTTGGTGATGTGTTAAATGCAGATCCTTAAAAAAGATTTGTGTTAAGGCCAAATACAATAGCTTATGGTCTTATAAGATAATGGAGCAAGTTTTTGTAGACATGGACTTAAATCATTTTGAATTTTACATCGGTGGCTTTGTTTCTGAAGACCTATTTCTGTCTGCATTTAAGTAGTAAACATAAATATTTTAAATTATACTGTCTCAAGATACTGGTTGTTGAAGTAGAACTAATTTTATATGTATTAAAAAACCAAATCTAGACAGTAACTTTCAAGAAAAGGTGGCATACAAATTTGACAGCATTCTTTGCAGACTTAAAATCCTAAGGTTTCTTCTCTTTATTAACTGTACTTTTTATAATTTCAGATAAGAATAATAGTGTGGATCATATAATGTCCAGATTTTGCTCTGCTTTTGGGTTAAAACTTTATTTAAGTTGTAGAGATGAGGTATAGAGAGCCTATGTATCATAAGTTCTTCTGTCTTCATTTAG
Seq C2 exon
GATTTGACGAAACGATCAAGTCAAACACAGAATAAAGCCAGCAGGAAGAGACAGCATGAGGAACCAGAAAGCTTCTTCACCTGGTTTACTGATCATTCTGATGCAGGTGCAGATGAGTTAGGAGAGGTCATCAAAGATGATATTTGGCCAAATCCATTACAGTACTACTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020959:ENSBTAT00000027913:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.474 A=NA C2=0.947
Domain overlap (PFAM):
C1:
PF0095613=NAP=FE(18.9=100)
A:
NA
C2:
PF0095613=NAP=FE(28.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTTGATGAAAACCCTTACTTCGA
R:
AGTACTGTAATGGATTTGGCCA
Band lengths:
278-847
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development