MmuINT0111776 @ mm9
Intron Retention
Gene
ENSMUSG00000052533 | Nup188
Description
nucleoporin 188 [Source:MGI Symbol;Acc:MGI:2446190]
Coordinates
chr2:30181970-30183107:+
Coord C1 exon
chr2:30181970-30182098
Coord A exon
chr2:30182099-30182967
Coord C2 exon
chr2:30182968-30183107
Length
869 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
CCACACACCCAGCCTGCCTTCCCTCTGCATCTGCAGCCTGGCTTATACCGAAGCTGGACAGACCGTCATTAGCATCATGGGAATTGGTGTAGACACCATAGACATGGTGATGGCTGCTCAGCCCCGCAG
Seq A exon
GTAGGGCCTCCTTTGTGCCCATCCCGTTGACCTTCAGACCCCATCTTAGCTTAACTTGTAGTTGCTTTGTTTGTTTTTCCATCTTTTTAAAATTAAAATATAATTACATCATTTTCCTCCTTCCCTTTCCTCCCTTCATCTCCTTCCACACCATCCCCTTGTACTCCTTCAAATTGATGTGTAGTTAAATACACACATGCCTACACACATACACATGCCCAGTATGTGTGCATAAATCTATAAACACAACCAGCTCTGTACATTTGGTGTACCTTCTGTACATATGGTTTCAGGGCCGAGCCATTGGTGTTAGTTAATAAATCCGAGCTCTGGGTTCTGGGCTCTTGGCTCTCAGCACTCCTTATTCACCTGCAGTTCTTTGTTTAAGCCTGGAGCCACAGTGAGCTTTCCCCATTCCTCTCTAGCATGACTGTTGGTATTATGTTCCTTCAGGTCTTGTTTAGGCAGCCGTGTTGATAGAGTATCATGGGTGAAGCTTCATTTTTTTAAAAGACTATCTTATAACAGCTTTCCTGGTCCTTGCAGTTGCTTTTTAAAAATAACTTTGTGGCCAGGTGGTGGTGGCAGGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGTGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCTAAACACAAAAACAAAAAACTCCTTGTATTTCCTAGCTAGTGGCTGCTGCATAGCTTCCTTCCTTTCCTAGTCTGAATTGGGCTTCTACTGTAGTCGGCTCGTGAGAGCACATCCTGACTGAGACCATCTTATTGGAACTAACTGTGATCTCCATTTGGCACCTAG
Seq C2 exon
TGATGGGCCAGAAGGCCAAGGCCAGGGCCAACTGCTGATCAAGACAGTGAAGCTGGCGTTCTCTGTCACCAACAATGTTATTCGGCTGAAACCTCCTTCTAATGTGGTTTCACCCCTGGAACAGGCTCTCACACAACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000052533-Nup188:NM_198304:23
Average complexity
IR-C
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(5.0=100),PF118943=DUF3414=FE(13.4=100)
A:
NA
C2:
PF104874=Nup188=FE(5.4=100),PF118943=DUF3414=FE(14.6=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:
CACACCCAGCCTGCCTTC
R:
GTTGTGTGAGAGCCTGTTCCA
Band lengths:
263-1132
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: