RnoINT0102257 @ rn6
Intron Retention
Gene
ENSRNOG00000018835 | Notch2
Description
notch 2 [Source:RGD Symbol;Acc:3188]
Coordinates
chr2:200243345-200245483:+
Coord C1 exon
chr2:200243345-200243604
Coord A exon
chr2:200243605-200245147
Coord C2 exon
chr2:200245148-200245483
Length
1543 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
TTCTGTTGCCCTTCCCTTAGGAA
3' ss Score
9.75
Exon sequences
Seq C1 exon
ATGTCCAGAGGGCTTCTTGGGAGAATATTGTCAACATCGAGACCCTTGTGAGAAGAACCGCTGTCAGAATGGTGGTACTTGTGTGACGCAGGCCATGTTGGGAAAAGCCACCTGTCGATGTGCTCCAGGGTTCACAGGGGAGGACTGCCAATACTCGACCTCTCACCCCTGTTTTGTTTCCCGCCCCTGTCAGAATGGAGGTACCTGCCACATGCTCAGCTGGGACACCTATGAGTGCACCTGTCAAGTTGGCTTCACAG
Seq A exon
GTAATGTGTCTGACTTTCCGGTGTCTGAAGTGACCTGTGTTAGCTACTTCTCGCTGTTGTGAGAGAACACCTCGATCACAGCAACTCCGAGAAGCAAGACTTTGCTTTCTGTTATGGTTCTAGAGGATGGATCCATAGTAGCTAGGAAGGCATGGCGGCCGTCAGAAAGTTGGCTGGTCAGTTTTCACTCACCAGTACAAAGCAGAGCAGGGCAGAAGTGGGAGGAGACTGCAAGCTCACAGCCTGCCCTCATCCATGTGCTTCCTGTAGTAGGGTCTCCATCTCTTAACAATTCTGTAACCTCCCCAAACGTACTGCCAACTGAGGACCAAGTGCGTAGATGCTTGACTCTGTGAGGGATATTTCTCCTCACATCAGGGCCCCCAACTCCACTGTACATTTAGCATTATGATACAAGTTGGAATATGGGGAAAGGTTCAGGGACACTTAAAAATCTGTTAACAGCTAAGTGTTAGCTATATAAACAGGAAAAGGTTAAAAATATGATTAAGAGGACATAAAATGGGGGTTGGGGATTTAGCTCAGTGGTAGAGCTCTTGCCTATCAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCGAAAAAAAGAAAAAAGAAAAGAAGAAAAAAAAAAGCGGACATAAAATGTGTGAGATCCTTTATATAGTATAGAAGAAAATAATTCAAGAATAACGTTCTTGGGGTTGGGGATTTAGCTCAGTGGTAGAGCGCTTGCCTAGGAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCTGAAAAAAAGAACCAAAAAAAAAAGAATAACGTTCTTAAACATTTTCATATTGAGGCACTGAGAATCTTTTAATTTGTAAGATGAACAGTCAGCGTGTCCTCTACCTTTGGAGAGTTTGAAGGTACAGGGGAGGAAAAAGAAAAAAGGTAGATACCTTGAAGTATTTGCTTAGACACTCAGGAAAATTGTTTGAAGAAAATGTAGTGTTGACTTGTTTCCGTCACTGAAGAGCAAACTCAGTAACCATATAGTGTGGAAAATCCACGTTTTCTTCACTAGCGAACGTGATTGAGAGCCTGGTGGGGACCCAGCCTCGTTGCTGTGGTGGCTGGCATGCGCTGAGGAGATGGCACGCTTCAGGGTGGGCATCAAGGATGGTTTGAAGAGGTGGCAGAGTTGTCAGCATAAGGGGGAGCCCAGCAGGTAAATGACAGTGTTCCCAGCAACGACCAGGAGCTAGGAGAGCAGGCAGACCCGAGCCTGGGCCACAGGACTGATGGAATGCTACCGGCATGGCTTTACGTAGCCAACATGAGTCCCTCATGTGCCCTGCCCCTGAATCTTTGAGTCTTACCGTACGGCCTCAGGGAACTTTGAGAAAACACCATTTGGTTGAGGATCTTGAGGTGGCACTCCTGTCCTCTGTAGATTCTGAAGTCTAGGGGTCTCCATGTAAGCAGATTGTTCTTCACTTGGTGGCAGAGGGAGCTGCTGAGTGTGGGCCTGGCTCCCTCAGGGAGTGGCACTGAGTTCTGTTGCCCTTCCCTTAG
Seq C2 exon
GAAAGCAGTGTCAGTGGACAGATGTCTGTCTGTCTCATCCCTGTGAAAATGGAAGCACCTGTAGCTCTGTGGCCAACCAGTTCTCCTGCAGATGTCCTGCAGGCATCACAGGCCAGAAGTGTGACGCCGACATCAATGAATGTGACATTCCAGGACGCTGCCAACATGGAGGCACCTGCCTCAACCTTCCTGGGTCCTACCGATGCCAATGCCCTCAGGGCTTCACAGGCCAGCACTGTGACAGCCCGTACGTGCCCTGTGCACCCTCACCCTGCGTCAATGGAGGCACCTGCCGTCAGACTGGAGACTTCACTTCTGAATGCCATTGCCTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018835:ENSRNOT00000025718:3
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=WD(100=37.5),PF0000822=EGF=PU(90.9=34.1)
A:
NA
C2:
PF0000822=EGF=PD(6.1=1.8),PF0000822=EGF=WD(100=27.4),PF0764510=EGF_CA=WD(100=38.9),PF126612=hEGF=PU(46.2=5.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATGTGCTCCAGGGTTCACAG
R:
GGTAGGACCCAGGAAGGTTGA
Band lengths:
345-1888
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]