RnoINT0102248 @ rn6
Intron Retention
Gene
ENSRNOG00000018835 | Notch2
Description
notch 2 [Source:RGD Symbol;Acc:3188]
Coordinates
chr2:200295602-200297313:+
Coord C1 exon
chr2:200295602-200295786
Coord A exon
chr2:200295787-200297180
Coord C2 exon
chr2:200297181-200297313
Length
1394 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
ATGTCCTTCTCTCCTGGCAGTGT
3' ss Score
10.48
Exon sequences
Seq C1 exon
GAGTACCTGTTGAACACTTGTGCCAGCACTCGGGTATCTGTATCAATGCTGGCAACACGCATCACTGCCAGTGCCCCCTGGGCTACACGGGGAGCTACTGCGAGGAACAGCTTGACGAGTGTGCGTCCAATCCATGCCAGCATGGTGCCACCTGCAGTGACTTCATCGGAGGATACAGATGTGAG
Seq A exon
GTGAGAAGGCGGCCGAGCTCACAGAGCTCCCGAGAGATGGTGCCGGTGCTAAAAACACTGGTTACTGAGTTCAGCCGTTAGTGTCCTGCAGAGTATCAATGTCTACTGTCCTTATGGTAGTGTTTAGCAGTCAGCGTTTTTATTTTCAGCCATGCTTTCCCGGAGCTCTGGTAAGATGTCTTCATAGAGTCTGGACCACCCCTCCTTAACTGGCTGACTCTCTATGTTGGCATCTTCCAGGCTAACCTGTGCTTCCTGAAGAGCAGCACAGTTCCAGCCAATGAGTAATTCTCTCAGACCAAAAAAAAAGTGTCTCACCTGCTGTACCACAGCACCGTGTTCAGCCTTAAACATTACTGTGCGTAATGTTTAAGCATGCGTCTTTTGTCAATGCCTGGGCTGACAGAAGTTAGAGCCAGATGTTAACCAAATACCACACTGGGAACCTGAAACCCACCAGACCACCAAGCAACAACAGAAGACCTCTCTCCTGCTGCCTTCAGTTGTTTATCTCAGAGCAGGCCTGGTCTGTTAGTTCAAAAGCCTGCCGATGCTGCACTCAAACTTTTACACATCTGACTGTTTTTAAATGAGCAGAATTACAGCCGTTTAGTATTGCCTGCCTGGTGTAGCCCACAGAGTAACACGCAGTGAGTGTATCCTAGGTAAGATCAGCTCTGGAATCCAAGGAGTCTAAACTCCCTCGGGAGCTCGCTCATGGAAAGACTATTGTTGCTGGGTCATTAAATGTCACCACACACAGTTTTAAGCTCCCGCCGTGGTATCCCCTCTTTCAAAGTTTGCTTCTCCCTTTACTCTGTAGTCTTGTGCTGTGAAGGAAGGACTTCTCTGCAGGCACTGTTGGCATTGTGGCACCTAAATGAAACTTCCCCACAGTTGTCTTTTTCCTTATCAAGTCTTGTTTCTTCCAACTCCTCCTGTATCGTCCACTGCCCTCCAAGGCCCACCACCCCCATGGCCCACTGCCTTCAGCCTCCTCATTTGCCCCAATTGTGCAATGGGCGCAGGGTCTTTACTACTGCAAGCACGTACTGTTTGAGCCTCTGGCTGCTTATCACCTGTGAAGGGGTGCGCAGTACACAGATGAGGAAATCCTTACCCGAAAGTTTTACTTGGGGGTCTCATGGAAGTGGCCCTCAGAACCTACGTCCTCGCTCTCCTTTAAAGTGACTTTGGGGGCGCGGGGCTGGAAGAGTGATAGGTAAGCGCAACCCTGCACTAGGAAGTAGTGAAGAATGCCATGGTTACAGAGGGATGGGTTCTCAGTTGCTCAGTGGGGTGGAAAGCAAAGCCATGGTGACCTGACCTCTCACTGGGCCCCATGGTCCGTCTCCGGTAGTGACCGCGTTCTCCATGTCCTTCTCTCCTGGCAG
Seq C2 exon
TGTGTTCCAGGGTATCAGGGTGTCAACTGTGAGTATGAAGTGGACGAGTGCCAGAACCAGCCCTGTCAGAACGGAGGCACCTGCATCGACCTCGTGAACCATTTCAAGTGCTCGTGCCCACCAGGCACCCGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018835:ENSRNOT00000025718:21
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=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=48.4),PF0000822=EGF=PU(67.7=33.9)
A:
NA
C2:
PF0000822=EGF=PD(25.8=17.8),PF0000822=EGF=PU(90.3=62.2)
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:
AGTACCTGTTGAACACTTGTGCC
R:
GGCACGAGCACTTGAAATGGT
Band lengths:
302-1696
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]