RnoINT0102312 @ rn6
Intron Retention
Gene
ENSRNOG00000000442 | Notch4
Description
notch 4 [Source:RGD Symbol;Acc:1303282]
Coordinates
chr20:4346890-4348447:+
Coord C1 exon
chr20:4346890-4347002
Coord A exon
chr20:4347003-4347923
Coord C2 exon
chr20:4347924-4348447
Length
921 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACT
5' ss Score
8.77
3' ss Seq
TTCTCTTCTCTCTGCCACAGGGT
3' ss Score
11.43
Exon sequences
Seq C1 exon
GCCAGCGGTGTGAAGTGGAGATGGACCTCTGCCAGAGCCAGCCCTGCTCCAATGGAGGGTCCTGTGAGGTCACAACAGGACCGCCCCCTGGCTTCACCTGCCGCTGCCCCGAG
Seq A exon
GTAACTGATTCAACACCCATTTCTCTCTTCTCCATCTACTGATGAGAGGTGAGAACACCAGAGCCAGGACGGAGGGCCATGAGTGGGGAGCGCTGGAGTCAGAATTACTGGAGAGGGCCCGAGTTCGCCCTGGTGAGTGGCTCTCAGAAACAGTCAGGGGAAAGGCAGAATCGAAAGGTAGCATGATGTAATTCTGTAGTCCCTGCCTTTGGGCATCGAGGCAGGAGGATGAAGGGTTCGAGGTCATCCTTGGCTACAACAACGAGTTCAAGCTGGTGAGATGGCTCAGCAGTTGAGGACGCTTGGCTGCTCTTCCAGAGGTCCTGAGTTCAACTCCCGGCAACCGCACGGTGACTCACAGTGAATCTGAGATCAGATTATCTCAAAAAAGCAAAACGAAACAAGAGACTGACCCTTCCAAGAATGGCTTCAGACAAGATCTCTAAACTGTGTGGGGGGACAGGTGTGGGTGAGGAACTCCTGGAAAGAAACTGCCTGAGGCCTTGGTTTGTGAAAACAGGGTATACCTTCTTTTCTCACCCTGATGCCCTTAAGCCAAACCCAGGAATGCTGATAGTAAACACATCCCCCTATTTTCACCTTCCTCTCATTTACCCCAAGCGTGTGGCTTGTCTCCAAGGATTAAAATGACACAGTAATCAGTCAACTGCGCCAGGCAGTGATCAGTCTTCTTGGACTTGCACCCTGAAACTACACATGGCTACACAGCCACATTTCATACCGAGGGCGATATGCCATTGTGTGCAGTTAGCAGGGACCTACCAGCGACATCCGTTACAAGGGACTCTCTGAGGTCCCTGCTACGTATGATAGTCTAGAACCCTCTGTCCCATGCTGTCCTAGCTTGCTTCAGGAAAGAATAATGTAAGGTTTTTTCGAATTCTCTTCTCTCTGCCACAG
Seq C2 exon
GGTTTTGAAGGCCCCACCTGCAGCCGCAAAGCCCCTGCCTGCGGCAACCATCATTGCCACAACGGAGGCCTATGTCTGCCCTCCCCTAAGCCAGGCTCCCCACCCCTCTGTGCCTGCCTCAGTGGCTTCGGGGGCCCTGACTGTCTGACACCTCCAGCTCCACCAGGGTGCGGTCCTCCCTCCCCCTGCATGCACAATGGTAGCTGCACTGAGACCCCCGGGTTGGGCAATCCTGGCTTTCAATGCACCTGCCCTCCTGACTCTCCGGGGCCCCGGTGTCAAAGGCCAGGGGCGAATGGATGTGAGGGCCGAGGTGGCGATGGAGCCTGTGATGCTGGCTGCAGTGGCCCAGGAGGGGACTGGGATGGAGGGGACTGTTCCCTGGGGGTCCCAGACCCCTGGAAGGGCTGTCCCCCGCATTCCCAGTGCTGGCTTCTCTTCCGGGATGGGCGGTGCCACCCACAGTGCGACTCTGAGGAGTGTCTGTTTGATGGCTATGACTGTGAGATCCCTCCAACTTGCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000442:ENSRNOT00000000513:20
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=PU(79.4=71.1)
A:
NA
C2:
PF0000822=EGF=PD(14.7=2.9),PF0000822=EGF=WD(100=20.6),PF0006612=Notch=WD(100=22.9),PF0006612=Notch=WD(100=21.7),PF0006612=Notch=PU(15.0=3.4)
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:
CAGCGGTGTGAAGTGGAGATG
R:
TTGAAAGCCAGGATTGCCCAA
Band lengths:
354-1275
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]