MmuINT0110058 @ mm9
Intron Retention
Gene
ENSMUSG00000015094 | Npdc1
Description
neural proliferation, differentiation and control gene 1 [Source:MGI Symbol;Acc:MGI:1099802]
Coordinates
chr2:25264127-25264521:+
Coord C1 exon
chr2:25264127-25264206
Coord A exon
chr2:25264207-25264424
Coord C2 exon
chr2:25264425-25264521
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-Npdc1:NM_008721:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.731 A=NA C2=0.848
Domain overlap (PFAM):
C1:
PF068096=NPDC1=FE(10.4=100)
A:
NA
C2:
PF068096=NPDC1=FE(12.9=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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: