BtaINT0128855 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020780 | SBNO2
Description
Bos taurus strawberry notch homolog 2 (Drosophila) (SBNO2), mRNA. [Source:RefSeq mRNA;Acc:NM_001077911]
Coordinates
chr7:45211061-45211395:-
Coord C1 exon
chr7:45211252-45211395
Coord A exon
chr7:45211156-45211251
Coord C2 exon
chr7:45211061-45211155
Length
96 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGC
5' ss Score
7.23
3' ss Seq
CACCCGCTCGCCCTCTACAGACC
3' ss Score
9.7
Exon sequences
Seq C1 exon
ACTGCTCCATCAGCAAGTTCCTGAACCGCATCCTGGGGTTGGAGGTGCACAAGCAGAACGCACTCTTCCAGTACTTCTCCGACACCTTTGACCACCTTATTGCCGCCGACAAGAGGGAGGGCAAATACGACATGGGCATCCTGG
Seq A exon
GTGAGCCCTGTGGGGACGCCCTCCCCTGGGCCAGGCCCCAGACTACCACTCGCCCCACTCACCCGCTCGCCCCACTCACCCGCTCGCCCTCTACAG
Seq C2 exon
ACCTGGCCCCTGGCATTGATGAGATCTATGAGGAAAGCCAGCAGGTGTTCCTGGCGCCTGGACACCCGCAGGATGGACAGGTGGTCTTCTACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020780:ENSBTAT00000027693:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF138711=Helicase_C_4=FE(17.2=100)
A:
NA
C2:
PF138711=Helicase_C_4=PD(0.1=0.0)
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:
AGCAAGTTCCTGAACCGCATC
R:
GAACACCTGCTGGCTTTCCTC
Band lengths:
183-279
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]