MmuINT0111777 @ mm9
Intron Retention
Gene
ENSMUSG00000052533 | Nup188
Description
nucleoporin 188 [Source:MGI Symbol;Acc:MGI:2446190]
Coordinates
chr2:30182968-30184933:+
Coord C1 exon
chr2:30182968-30183107
Coord A exon
chr2:30183108-30184826
Coord C2 exon
chr2:30184827-30184933
Length
1719 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGT
5' ss Score
8.35
3' ss Seq
ATCTGTTTCCTTTGCTTCAGGTG
3' ss Score
10.88
Exon sequences
Seq C1 exon
TGATGGGCCAGAAGGCCAAGGCCAGGGCCAACTGCTGATCAAGACAGTGAAGCTGGCGTTCTCTGTCACCAACAATGTTATTCGGCTGAAACCTCCTTCTAATGTGGTTTCACCCCTGGAACAGGCTCTCACACAACATG
Seq A exon
GTATGTGTTTTTCTTCCTCGGCTACGTTTCTGCCCATAAAAACATAGTTAACGCCCTCTGCTTGGACATCAGAAATCATTCTCAGCTCATTTCTTTAGGCTTGGTAACAAGGGACTGCATCATAGTTTATTCTGGACTCCTGCTGATGACATAGTAATACTTAAGGATGGAGACTGGGGTCATATTTCTTTGGTTCAGATTTAGGTTTTGCTCAGCTGTATGAGAACCTCAGGCATATTTAAGCTTTGTCTCAGATTTCTCATCCAGAATGGCACAGAAGTAAATTGCTGTATCCATGGGAGACTGAGGCAGGAGGATAAGCTCAGCTAGGGCTGCCTAACAAGTAGAGTGCTAGGCCATGCAAATGACTACAGTGTAGGAAGCTCCTTCCCTGTAGGGTGGGGAGGACGGCTCACACAGTCCCTCAAGGATGATGGCGGTGCTGACAGCAGTTACAAATGGGTGATTGATTGACTGCACAGAGGAGAGGGCCTGGCTCATGCCCACAGTCGCCCCTCTGCTCTCCAGAGGCAGAAGGGCCAGGGCCACCTGCTAGTCAAGACAGTGAAGACAGTGAAGCTGGCATTCTCTGTCACCAGTCCCTGACGGTCTGGTCTGTATAGCAAAATCTTTCAAAGACAAACAACCCTGAAAAAACAAGCACAAAAAGTCCTTCAAATCACATTGGCTCATATCAGTGTGACTCTAAGCTCGTTAATCTTTGGCTCACTTTCATTATGAGTAATGTTTTATATCATGTCTAAAAGCATTTATTTTTTTTCTTTTTTAATATTTTTAATTAGGTATTTTCCTCATTTACATTTCCAATGCTATCCCAAAAATCCCCCATACTCTCCCCCCCCCAAAAGCATTTATAACTTTAATTTTTTTCATTTGCTATGCTGGGGTCTGAACCCAGGGCCTTATTCGAGTTAGTAGGCGCTCCACTATTAAGTCACTGCTCTAGTACCAGTTATGCACAGGCTGGCCTTAAATTGATTATGTAGCCACGATGTCCTGGAATGCCCCCTCCCCTATACCCCTCCCCTGCCCCTTTGTTTCAATTTGTTACATTTGTTATATTTGTGTTCATGATGTCTGGGTGTCAGCTCTTTCTTTCCACTATGAGGGTTCTGGGAGTTGAGCTATGGTCATCAGGTTTAGCAGCAAGCACCCACTGGGCCATCTCAGTGACCCTTGCCCTTCAATTTTGGTTCCTCCTTTCTTCACCTTCCAAGTGCTGAGGTTACAAGTATGTGCTACTGTGTCTGCCCAGAGGGGTTTGTGTTTTCTGAAAGTGCATGTGTGTGTGTGGGGGGGGTGCGCGTGCATACTTGCATGTGAATGTGGAAGTCAGACTGTGGGGCTTGGCTCTCTCCCACCACCATGGAGGACTGACTCTGTCGTCAGACTTGGCAAGGAGCCTTCCCCACTGAACCTCATTGCCTTCCTGCTTAAGGGTTCAAGGCTTAAAGGTTCTTCTTTTCCTTTTTTAAAAATTTCAGTACAGTGCCTTTTGTAACCTCCTTATTAAAGAGTATTTCTTTTAAAATATATCTTTGTATTAATGCATTGTATTGAACTGTTTATCCCCAAATCCTAGTTATCTCTTTGCTACTGAGAATAGGACTGAACTGGCCACCTCTACTTAATCAGCCCCAGTGGCTGGTGTTTTGAAAGAACTGTAATGGGTCCCTGGATCTGTTTCCTTTGCTTCAG
Seq C2 exon
GTGCCCACGGGAACAACCTCATTGCTGTCCTAGCCAAGTACATCTACCACAGACATGACCCAGCCTTGCCACGTCTGGCCATCCAGCTGCTGAAACGCTTGGCCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000052533-Nup188:NM_198304:24
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.125 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF104874=Nup188=FE(5.4=100),PF118943=DUF3414=FE(14.6=100)
A:
NA
C2:
PF104874=Nup188=FE(4.1=100),PF118943=DUF3414=FE(10.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGGCCAACTGCTGATCAAG
R:
TGGCCAAGCGTTTCAGCAG
Band lengths:
223-1942
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: