MmuINT0110058 @ mm10
Intron Retention
Gene
ENSMUSG00000015094 | Npdc1
Description
neural proliferation, differentiation and control 1 [Source:MGI Symbol;Acc:MGI:1099802]
Coordinates
chr2:25408607-25409001:+
Coord C1 exon
chr2:25408607-25408686
Coord A exon
chr2:25408687-25408904
Coord C2 exon
chr2:25408905-25409001
Length
218 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGC
5' ss Score
8.02
3' ss Seq
AGCTATTTTGCTCCCACCAGGCA
3' ss Score
6.85
Exon sequences
Seq C1 exon
CCTGGGGATCAGCGGCTGGCACACAGTGCTGAGATGTATCATTATCAGCACCAGAGACAGCAGATGCTGTGCCTGGAGCG
Seq A exon
GTGAGCGTCCTGGTCTGAAGTGGCCGCTTTTCTCCTGCACCTGTGCCCCACCCACACCTCACCTGGCCATCCGTCCCTACCTGCTCGAAACCTCTTACTCTCTGCCCCGGCACCCCAGCCCACGGCCCCTACCCAGGGCAGCAATACATTGAGCACCCGCCTCTGGGCCCCTGTTCCTTGGAGAGGCACAGAGGACCCAGCTATTTTGCTCCCACCAG
Seq C2 exon
GCATAAGGAACCTCCAAAGGAACTAGAGTCAGCTTCCTCCGATGAGGAAAATGAAGATGGCGACTTCACTGTGTATGAATGCCCAGGCCTGGCGCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015094:ENSMUST00000071442:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.728 A=NA C2=0.848
Domain overlap (PFAM):
C1:
PF068096=NPDC1=FE(7.6=100)
A:
NA
C2:
PF068096=NPDC1=FE(11.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGGGGATCAGCGGCTG
R:
CCAGGCCTGGGCATTCATAC
Band lengths:
172-390
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types