BtaINT0102881 @ bosTau6
Intron Retention
Gene
ENSBTAG00000007909 | NOTCH2
Description
notch 2 [Source:HGNC Symbol;Acc:HGNC:7882]
Coordinates
chr3:23461805-23464094:+
Coord C1 exon
chr3:23461805-23461937
Coord A exon
chr3:23461938-23463857
Coord C2 exon
chr3:23463858-23464094
Length
1920 bp
Sequences
Splice sites
5' ss Seq
GGGGTATGA
5' ss Score
5.41
3' ss Seq
CCCTCCTCTCTCTCCTCCAGGCC
3' ss Score
13.52
Exon sequences
Seq C1 exon
TGTGTCCCTGGATATCAGGGTGTCAACTGCGAGTATGAAGTGGATGAGTGCCAGAACCAGCCATGCCAGAATGGGGGCACCTGTATCGACCTTGTGAACCACTTCAAGTGCTCCTGCCCACCAGGCACTCGGG
Seq A exon
GTATGAAATCAGCCTTACCTGTCTTCCATCCAGGGCATTCTCTAAGTTGTAAATGCATTTTTAGTCTCGTGAAGGGATTTTTAAAACAAGATTCAGCAGTATTCTGAATCTTAGAGATTCAAGCCATTTCATTGCTCTCTTGCCAAGCTCCGGTGTTCTAATGCCTGTTCTCAATTCTGTCTGGTTGTTGTTGAAACCCATGAAACACAGAATGTGCAAATGACATAATGTTGCAGCAAAGTTAATCTGGCTAGCAAGATCTCTTGGTGCTTCAAGGGAAAACAACCAGTAGCCTCTTGAATAAATTATTTGTATTTACCAGCTCGTGTATTTTTCTAAACTTCCAAGTCTTGCCTCCATAAAGTGGGAAAATGAATGAAATGAAAACATTTGCCTATTTTCGTAAGCCCAAGGGGAAAAGGTTGATGGTCCAAGAATGAACTAAGAATTACAATAAGACCTAATGAGATACAACCCTAGATGGTGGATGGTGGAGCCATCATTCCACCAGGGGCATTCTCCTGCCTGCAAACAATCTCCTGGAAAGAGCTTGGAGTATTATTTTTTAGAAGAGATGTAGTTATATGGTGCCTGTTCTGAGCAGCACGTCAAAAGAAAAAGCCATCCACAATGGTGGAAAATTGATTCTCATCAAAGAGAATAGAATGTTAGAGAAATATTTATACTGTCTTAAAGCTTTGGGTCAGTGAATTTTGGGTTTCCTTCTTGAGTTCAGAGTTGGCTAAATTAGAATGGAAAAGTGCCCCAGTAGTAGGCTCGTTATTGAGCAGTGAGATTAACAGGGAAGACAAAACTAAGGAGAAAGCCTTTAAATACTTGAAGATTTGTTCCATTAAAGGAGAGTTTTTTCTGCTCAGTACTTGAAAGAGAAGTAGAGGTTAATTTTAATTCTAGAGGTAATATTATCCATTAAAAATCCTGTTAATATTTTTATTGAGGTCACATTAAATTTACGAATTGGTATAAAGAAGACTGACATCTTTAGAATGAGGAGTCTTCCTAACCAACCCATTGTGTCTTTCTGTTTATTCAAGTTTCCTTTTGTGTCTTTTAGGTCTACTTTAAATTCTTCGTGTAGGTGTAGTACATTTCTTGTTAAGATTGTTCTTAGATATTTTATCTTTTGCTATTGCTATTGAAACTGAGGCCTTTTTTTTTAAATACATTTTTCTTTTCTTTCAAATAGTCTTGCTATTACAAGTGGTAAGAATACAGTACTGTTTTTCTTTCTTCTGTAATTTTTTGAATTAATCATGAAATCACTTATAGAATAGTCATTGATTTCTTTTATTTCTTCCTCAAAAATATGTACAGATGTTCATACTTGATGGCTCTTTTACATATATAACACATTAAATGAGTTCTGTTTTAAATGGCATAACCTTTGAGCTCTCAATAGGATATTTCCCTTCTATTTTTTTGATAAAAGATATTTGTGCACTTACACTATTTTACAGAAAAAGTCATTTGTGTAATTCAAAATTTACTTCCAATTCTTACCAGTGATTACTTGTAGTCTATTTATTTATGGTTATATTCTTTTTAACTGTTTTTATATTTTAAATCAAAATGAATACATTAATGAAAAGTTACCAAATCTCTCTTGAGTTCCAATTTCCTTACCTTTCAAGTGGAAAAATAATACTAGCTATGCCCTAAGGGATTGCTTCATCACTGGGTTGTGTGGGGAGAACATGAGAAGCCCTGAGTACATCCTTTGCTTACTGGTGTCCAAGAGAATGGGCACAATCCTGGGTCAAGCGTGTGTTAGGCCCTGCCTGACCGGAATGGTTCCAGCCTGACTAATTGTGGAAATGCCACCAGGGCTGGTTTTCCCTTCCTGGAAGGCAGCGTTCCAAGAACTGTAATAATTTTCTCTCCCTCCTCTCTCTCCTCCAG
Seq C2 exon
GCCTGCTTTGTGAAGAGAACGTTGACGACTGTGCCAGGGGTCCCCACTGCCTTAATGGTGGCCAGTGTGTAGACAGGATTGGGGGCTACAGTTGTCGCTGCTTGCCAGGCTTTGCTGGAGAACGCTGTGAAGGGGACATCAACGAGTGCCTGTCCAACCCCTGCAGCTCTGAGGGCAGCCTGGACTGCATACAGCTCACCAACGACTACCTGTGCGTCTGCCGCAGCACCTTCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007909:ENSBTAT00000010400:22
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(25.8=17.8),PF0000822=EGF=PU(90.3=62.2)
A:
NA
C2:
PF0000822=EGF=PD(6.5=2.5),PF0000822=EGF=WD(100=40.0)
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:
GGATATCAGGGTGTCAACTGCG
R:
CAGACGCACAGGTAGTCGTTG
Band lengths:
344-2264
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]