RnoINT0102287 @ rn6
Intron Retention
Gene
ENSRNOG00000004346 | Notch3
Description
notch 3 [Source:RGD Symbol;Acc:620761]
Coordinates
chr7:14158120-14159660:-
Coord C1 exon
chr7:14159438-14159660
Coord A exon
chr7:14158205-14159437
Coord C2 exon
chr7:14158120-14158204
Length
1233 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGA
5' ss Score
6.42
3' ss Seq
TCTTCCTGTTTTCCCCCAAGGAA
3' ss Score
9.58
Exon sequences
Seq C1 exon
GAGAGCCCTTGGAGCCTCCAGAGCAGAGCGTGCCACTGCTGCCGCTGCTGGTGGCAGGGGCTGTCTTTCTGCTGGTCATCTTCGTCCTGGGTGTCATGGTTGCCAGGCGCAAGCGAGAGCACAGCACCCTCTGGTTTCCTGAGGGTTTTGCATTACACAAGGACATAGCTGCTGGCCACAAGGGCCGGAGGGAGCCCGTGGGACAAGACGCACTGGGCATGAA
Seq A exon
GTAAGAACCTCGTCTGCTCTATGTCCCCAGTGACGTGGCCCTTGCAGACTCTGGATCGGACCCACCTGGGTCATATCCCAACCTCCGACCCTAACCTAACTAACTCAGATTCCATCTGGGGCTTCGGTGTTAACCCTCTTGACCTGTGAACCGATGACCCCTGAGCCCTGACCCTTGACTTGATCTCTGACTCGTATCTTCCCCTGAACCAGCCACACCAAATCCATCCCAGTTCATTCCTGCATGACTTTTGTCATCTCAACTTGTCCCTGACCGGGAGGGCTGTGTCTTTGATGACTCCTGAATCACCTCTGGCTTTGACCTACCTGTGCCTTTGACCTCACCTCAGACCTCTGCCTCCACCCGATCCTGAGTTAATTCCCCCGTGAACCCTAGTCTCAAGCCTTCAACTTGACCTAGCCCTCAGTACCTACAACCATATTCCAGTCTCAACCCTTCCCCATGACACCACAACTCCTGACTCCGTATCATGACGTTTCCACCTAGGCTATCCTGTTTGTCATGAGAGCAACTCCTTTTCCATGAGCTTTGATCACTTCCTCTACAAAGTCATGAGAGGACAACGTCCTCTGTCCCCTGCTGGTTGCCCCATCTATCCTCAACTAACCACGTTCCTTTGTGTGTGCCACTCCCGCCTCTGAGTTCACCTTGAGATTCTGGCTGCCTCGGACTTGAGGTGTGGCTCAGAACTTTAAGTGATTGTTGAGCAGATGTGAAGACCAGAGTTTGGATCCCTAGGACCTGTATAAATGCCATAAAATCCTTAAATGCCCAGTGGGCACGGCAGCCTGACTTGGTAGATGGAGTCCTGGTCCCTAGAGCAAGCTGATTAGTGAGTCCTTTCATATCAGTGAGCTCTTGGTTTGATTGAGAGACCCTGCCTCGATGACCAAGACTGAGGAGAGATTGAAGATGATTCCTATTCATCAACCTCATTCCTGTATACCTACATGTACGGCTGGGCACCCAAAACACACACATGTACACACAGATGAAAACATTTTGATTGCCACCTGACATGATTCCTGCAACCTCATCGATATCCTTCTATCCACCATTGGAATCTTTGTCAACAGCCCAGAACCCCTCCTCAATTCCTGACCCCTGACCTGCCTCTATGACCTCTGCTTGAACTGAACCCTCAATCCTCCTCCCAGGCCAGATGTGTCTAGTGCACTTTCTCACGCCTTTTTCTTCCTGTTTTCCCCCAAG
Seq C2 exon
GAACATGACCAAGGGTGAGAGTCTGATGGGGGAGGTGGCCACAGACTGGAATGACTCAGAATGCCCAGAGGCCAAGAGACTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004346:ENSRNOT00000037456:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.240 A=NA C2=0.793
Domain overlap (PFAM):
C1:
PF076847=NODP=PD(13.8=12.0)
A:
NA
C2:
NO
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:
GAGAGCCCTTGGAGCCTCC
R:
TTCAGTCTCTTGGCCTCTGGG
Band lengths:
307-1540
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]