RnoINT0104200 @ rn6
Intron Retention
Gene
ENSRNOG00000025185 | Nup188
Description
nucleoporin 188 [Source:RGD Symbol;Acc:1306022]
Coordinates
chr3:8891538-8892631:+
Coord C1 exon
chr3:8891538-8891666
Coord A exon
chr3:8891667-8892491
Coord C2 exon
chr3:8892492-8892631
Length
825 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
GATCTCCATTTGGCACCTAGTGA
3' ss Score
3.24
Exon sequences
Seq C1 exon
CCACACGCCCAGCCTGCCTTCCCTCTGCATCTGCAGCCTGGCTTATACCGAGGCTGGACAGACTGTCATCAGCATCATGGGAATTGGTGTGGACACCATAGACATGGTGATGGCTGCTCAGCCCCGCAG
Seq A exon
GTAGGGCCCCCTCTGTGCCTGCCTCGTTGACCTTCAGACCCATCTTAGCCTAACGTGTAGTCGCTTTGTTTGTTTTCTCATTCCCTTTTCTCCCTCCAACTCCTTCCACACCCTCCCCTGTACACCTTCAAATTGATGTGTTGTTAAACACACAAATGCCTACACACATAACCTGCCCAGTGTGTGCTCATAAATGTATAAATACAGTCAGCTTCGTACATTTGGTGTTGCCTATATGTCTATGATTTCAGGGCTGAGCCATTTGTGTTAGATAATAAACTGGCGGCTGATCTCTGGGAAAGACTAGTTCTCCTGCTGTCTGCCTTCCTTACTTACCTGCAGTCCTTTGTTTAAGCTGGCCCACTTGAGCTTCCCTGTCTTTAGCAAGTCTATTGGTATAGTAATCCCTTCAGGGCTTGTGGAGGCCGCCAAGCTGATGGGGTACCCTGGGGGGTGTTTCCTTTCTCTTTTTGTAAAGACAATCTCATAATAGCTTTCCTGGTCCTTGCAGTTTTGTTTTGTTTTGTTTTAATAACTTTGCGGCAAGATGGTGGTGGCAGGCCTTTAATCCCAGAATTTAGGAAACAGGTAGGTGAGTCTCTGAGTTTGAAGCCAGCCTGGTCCAGAGCAGCCATGGCTACACAGAGAAACCCTGTCTCCAAACACGAAAACAAAAAACTGTGGTATTTCCTAGCTAGTGGCTGCTGCATAGCCTCTTCCCTCTCCTAGTCTGAATGGGGCTCCTACTGCAGTCTGGCTCGTGAGAGCACACCCTGACTGAGACCGTCTTATCGGAACTAACTGTGATCTCCATTTGGCACCTAG
Seq C2 exon
TGATGGGCCAGAAGGTCAGGGCCAGGGCCAACTGCTGATCAAGACAGTGAAGCTGGCGTTCTCTGTCACCAACAATGTTATTCGGCTGAAGCCTCCTTCTAATGTGGTGTCCCCCCTGGAACAGGCTCTCACACAGCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025185:ENSRNOT00000030996:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.068 A=NA C2=0.125
Domain overlap (PFAM):
C1:
PF104874=Nup188=FE(5.9=100),PF118943=DUF3414=FE(8.6=100)
A:
NA
C2:
PF104874=Nup188=FE(6.4=100),PF118943=DUF3414=FE(9.4=100)
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:
CCCAGCCTGCCTTCCCTC
R:
CATGCTGTGTGAGAGCCTGTT
Band lengths:
262-1087
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]