BtaINT0128863 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020780 | SBNO2
Description
Bos taurus strawberry notch homolog 2 (Drosophila) (SBNO2), mRNA. [Source:RefSeq mRNA;Acc:NM_001077911]
Coordinates
chr7:45220637-45222265:-
Coord C1 exon
chr7:45222104-45222265
Coord A exon
chr7:45220721-45222103
Coord C2 exon
chr7:45220637-45220720
Length
1383 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
TGCCTCTCTCTCCTCTCCAGCTG
3' ss Score
10.93
Exon sequences
Seq C1 exon
GACTCCTCATACCTCGATGACCTCTCCAACGCTTCCATCTTCTCCTCATCCGTGGACTCCCTCTCGGACATAGCCGACACGCCTGACTTTCCGCCCGCTGACAGCCTCAGCCAGGTGCCTACCATCTGGGACGTGAGCACCGGCCCCTCCGCCCACGACAAG
Seq A exon
GTCAGTGCGCCCAGCCTCCAAGCTGGCAGCCATGCCAAGGCCACTCAGACCCAGACAACACTGCTACTCAAGGTTGCTCCTGTCTCCTATGTGGGCCTAAAGATGCAGGGGCTACCAGGGGGAAGGGGGACTCTGGGGAGCACAGCACACACTAGTGGATATTGGTGGATATCTGCCCAGCTGCCTGACAGGTTCAGTGCCTGTGAAACCCCTGGACCCTCAGGAAGGGTTAGGGAGATGTGACATGCCCAGAGCAGGTGCAGTAGGCAACGCAGGCCCAACCCACCTCTGGCTGCAGGGGCCCAGTGGGGCAGTAACCCTGCCCTCCCCTCACCAGGGCCCTCCCACCAGCTCCTAGCCTCTGCCAGGCCCAAGCGGGCAGCTGAAACCCCACACGTACTCCTGCTGCGGCCAGCAGGGCTGCAGGAACCTGACTCAGCCTTCCAGGAACCTGAGCCCGAGGCTGTTTGTTTGTTTTTGTTAATTAAAAAAAAAAAAAACGGGAGAGGGAATTGAGGGTAGGTTTCTGATCTCCTTGTACCTCATTTCCATTTTATTTTCATTTCAAGAAAACTTTGTGTGTTTTTTTTTTTTTTTAACTTCCCTGGTCCAGGGGCTAAGATTGTGCTTCTGCCATAGGGAAACACAGGTTTGATCCCTAGATGGGGAACTAAGATGCCGCATGCTGCACAGCACAGGCCCCCCCCCTCCAAAAAGAAAAGAAAAGGAAACTACACTTTGATTAAAAAAACAAAAGTTTGTTTTTACTTTCCTTCCAGTTTTATTGAGATGTAATTGACACATGGCACTAAGTTTAAGGTGATGCCCACACAGCACAACGATTGACTTGCATATGTCATGAAAAAGGACCACAATAAGTCAGTGAACATCCACTGTCTCGTATCGATATAACGATAAAGAGATAGAGGGACTTCCCTGGTGGTCCAGTGGTTAGAACTTGGCACTGTCACTGCTGGGGGCCTGGGTTCAATACCTGGTTGGGGAACTAAGAGCCCACAAGCCACACAGCATAGCCAAAAGAGGAAAAAAAAAAAAGTAGAAAACCTCTTTTTTTTCCTTGTGCCTAGAACTCCTTGCATTTACTGTTAATTTTCATATACAACGTACAGCAATGTTGTCTACTTATCATGCTGCCTCTTGCGTTCCTAGTTCTTATGTGTCTAGTGCTTTGTATGCCCCTAGTACTTATTTATGCAGCAGATCTAAGCAGGCAGACAGCAGGAGGGAGGCTTGTAGCCAGCTGAGGGGCTTGAGGACAATCAGGCGAGCCCTCCTGGAGGCTGGGGGCCTATCCAGGCACTTCAGCCCCACCTCTGGCCTGCAGGCTCATGCCCCCTCTCCCTGCCTCTCTCTCCTCTCCAG
Seq C2 exon
CTGTTCCCGCCCAGTGGGACATTTACAGGCCTCGAGGACCCTGTGTCCTCCCTCTCCAGCACCCCACTTCTCATCAGCTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020780:ENSBTAT00000027693:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.556 A=NA C2=0.714
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACTCCTCATACCTCGATGACCT
R:
CTGGTAGCTGATGAGAAGTGGG
Band lengths:
246-1629
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]