BtaINT0102904 @ bosTau6
Intron Retention
Gene
ENSBTAG00000043971 | NOTCH3
Description
notch 3 [Source:HGNC Symbol;Acc:HGNC:7883]
Coordinates
chr7:8942977-8943397:+
Coord C1 exon
chr7:8942977-8943169
Coord A exon
chr7:8943170-8943245
Coord C2 exon
chr7:8943246-8943397
Length
76 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGG
5' ss Score
7.13
3' ss Seq
CTGACTGCCTCCCTCACCAGGTT
3' ss Score
10.23
Exon sequences
Seq C1 exon
GGCCCCTCTGCAACGTGGAGATCAACGAATGTGCGTCCAACCCCTGCGGCGAGGGAGCCTCCTGCGTGGATGGTGAAAATGGCTTCCGATGCCTCTGCCCACCTGGCTCCCTGCCCCCACTCTGCCTTCCCCCAAGCCATCCTTGTGCCCAGGAACCCTGCAGTCATGGCGTCTGCCACGATGCGCCTGGAGG
Seq A exon
GTGAGGTCTCTCCCCAGATCCCTGACCCCCACAGCTTCCCTACCCTCCTGCCAGCCCTGACTGCCTCCCTCACCAG
Seq C2 exon
GTTCCGCTGTGTGTGTGAGCCTGGCTGGAGTGGCCCTCAGTGCAGTCAGAGCCTCACTCGAGATGCCTGTGAATCCCATCCCTGCCGGGCAGGCGGCACCTGCACCAGTGATGGAATGGGCTTCCGCTGCACCTGTCCCCCTGGTGTCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000043971:ENSBTAT00000060960:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=PD(6.7=3.1),PF0000822=EGF=WD(100=41.5),PF0000822=EGF=PU(53.3=24.6)
A:
NA
C2:
PF0000822=EGF=PD(43.3=25.0),PF0000822=EGF=PU(90.3=53.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAATGGCTTCCGATGCCTCTG
R:
TCTCGAGTGAGGCTCTGACTG
Band lengths:
180-256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]