RnoINT0102313 @ rn6
Intron Retention
Gene
ENSRNOG00000000442 | Notch4
Description
notch 4 [Source:RGD Symbol;Acc:1303282]
Coordinates
chr20:4347924-4349280:+
Coord C1 exon
chr20:4347924-4348447
Coord A exon
chr20:4348448-4348896
Coord C2 exon
chr20:4348897-4349280
Length
449 bp
Sequences
Splice sites
5' ss Seq
CACGTGAGC
5' ss Score
5.62
3' ss Seq
CACGTTCCCTTTGCCCGCAGCCC
3' ss Score
11.17
Exon sequences
Seq C1 exon
GGTTTTGAAGGCCCCACCTGCAGCCGCAAAGCCCCTGCCTGCGGCAACCATCATTGCCACAACGGAGGCCTATGTCTGCCCTCCCCTAAGCCAGGCTCCCCACCCCTCTGTGCCTGCCTCAGTGGCTTCGGGGGCCCTGACTGTCTGACACCTCCAGCTCCACCAGGGTGCGGTCCTCCCTCCCCCTGCATGCACAATGGTAGCTGCACTGAGACCCCCGGGTTGGGCAATCCTGGCTTTCAATGCACCTGCCCTCCTGACTCTCCGGGGCCCCGGTGTCAAAGGCCAGGGGCGAATGGATGTGAGGGCCGAGGTGGCGATGGAGCCTGTGATGCTGGCTGCAGTGGCCCAGGAGGGGACTGGGATGGAGGGGACTGTTCCCTGGGGGTCCCAGACCCCTGGAAGGGCTGTCCCCCGCATTCCCAGTGCTGGCTTCTCTTCCGGGATGGGCGGTGCCACCCACAGTGCGACTCTGAGGAGTGTCTGTTTGATGGCTATGACTGTGAGATCCCTCCAACTTGCAC
Seq A exon
GTGAGCCTTGGGAGTGAGGGGTGGGTGAGGGTCGAGGGTGGGGAGACATACATGCCCGCCCGAGTTACAGAGTGACCAGCATTGGACTCCAGGGGGCTTCCATGCTAAGAAAGACTCTAGGTTCCAATCCAGAGGAATGGAGTGAGAGACACTGTGGGACACAGGCTTGGTCTCCACTCCTGAGAACGCTAAGGCCTCAGACCTCAGCGTCTCTTCCCCGGCCCTTCCACCAAAGGATGCCTCCCTGGCAAGCAACACCCCCAAGAGAAAGGGTCTTGGGCCCTCTTTCTGAGACAGGGGCAGGAGGAAAGGTTGGCCCCAGTAAGCGGGGGTCAGCAGATAGCAACCTTAGCAACCCAAGTCCCAGAGGCAATGGAGGGGCCGTAATTCTCTGTGAAGAAGGGTCAGATTTGGGGAGAGTGCTGAGTCCACGTTCCCTTTGCCCGCAG
Seq C2 exon
CCCAGCCTACGACCAGTACTGCCGAGATCACTTCCACAACGGGCACTGTGAGAAAGGCTGCAACAACGCTCAGTGTGGCTGGGATGGGGGTGACTGCAGGCCAGAAGGGGATGACTCAGAGGGGGGCCCCTCCCTGGCCCTGCTGGTGGTGCTGAGTCCCCCAGCCTTGGATCAGCAGCTGCTTGCCCTGGCTCGAGTACTGTCCCTGACTCTGAGGGTCGGTCTCTGGGTGAGGAAGGACAGTGAAGGCAGGAACATGGTGTTCCCCTATCCTGGGACCCGGGCCAAAGAGGAGCTGAGTGGAACTAGAGATTCCTCTTCGTGGGAAAGACAAGCCCCTCACACTCAGACCCCGGGCAAAGAGACAGAGTCCCTTGGTGCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000442:ENSRNOT00000000513:21
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=0.333
Domain overlap (PFAM):
C1:
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)
A:
NA
C2:
PF0006612=Notch=PD(82.5=25.6),PF068168=NOD=WD(100=39.5),PF076847=NODP=PU(3.1=1.6)
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:
TCCTGGCTTTCAATGCACCTG
R:
CTTTCTCACAGTGCCCGTTGT
Band lengths:
350-799
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]