BtaINT0102902 @ bosTau6
Intron Retention
Gene
ENSBTAG00000043971 | NOTCH3
Description
notch 3 [Source:HGNC Symbol;Acc:HGNC:7883]
Coordinates
chr7:8942030-8942494:+
Coord C1 exon
chr7:8942030-8942263
Coord A exon
chr7:8942264-8942383
Coord C2 exon
chr7:8942384-8942494
Length
120 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
GTCATGTTCCCCTTCCGCAGGTG
3' ss Score
11.29
Exon sequences
Seq C1 exon
GCTTCGAGGGCACAGTGTGTGAGCGCAACGTGGATGACTGCTCGCCTGACCCTTGCCACCACGGGCGCTGTGTGGACGGCATCGCCAGTTTCTCGTGTGCCTGTGCCCCGGGCTATACAGGCATGCGCTGTGAGAGCCAGGTGGATGAATGCCGAAGCCAGCCCTGCCGACATGGGGGCAAATGCCTAGACCTGGTGGACAAATACCTCTGCCGCTGCCCTCCTGGCACCACAG
Seq A exon
GTAGGGCCAGGAGCTGGGCTGGGACAGGAATAGTACATCTGATGGGACACAGAGGGTTCAGGAATGGTGTTTCTGGCAGGTCACGGTGGTGGCAATCCCAGTCATGTTCCCCTTCCGCAG
Seq C2 exon
GTGTGAACTGCGAGGTGAACACTGATGATTGTGCCAGCAACCCCTGCACCTTTGGAGTCTGCCGGGACGGCATCAACCGCTATGACTGTGTCTGCCAGCCTGGATTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000043971:ENSBTAT00000060960:11
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:
PF0000822=EGF=PD(13.3=5.1),PF0000822=EGF=WD(100=38.0),PF0000822=EGF=PU(90.3=35.4)
A:
NA
C2:
PF0000822=EGF=PD(6.5=5.3),PF0000822=EGF=PU(90.0=71.1)
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:
CCAGTTTCTCGTGTGCCTGTG
R:
CTGGCAGACACAGTCATAGCG
Band lengths:
248-368
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]