MmuINT0110053 @ mm9
Intron Retention
Gene
ENSMUSG00000015094 | Npdc1
Description
neural proliferation, differentiation and control gene 1 [Source:MGI Symbol;Acc:MGI:1099802]
Coordinates
chr2:25261735-25263256:+
Coord C1 exon
chr2:25261735-25261881
Coord A exon
chr2:25261882-25263115
Coord C2 exon
chr2:25263116-25263256
Length
1234 bp
Sequences
Splice sites
5' ss Seq
CTGGTATGG
5' ss Score
7.13
3' ss Seq
TGGCCCATCACACTCCTCAGGGG
3' ss Score
4.51
Exon sequences
Seq C1 exon
ATGCTACCACCTGTCCTGGAAGCCTGGATTGTGCACTGAAGAGGCGGGCAAAATGCCCACCAGGGGCACATGCCTGTGGACCATGCCTTCAGTCCTTCCAGGAAGACCAGCGAGGGTTCTGTGTGCCAAGGAAACACCTATCTTCTG
Seq A exon
GTATGGCAGAGTATAGAATTAAGGGAAATGGATGTGTGGCATGTGTTTCCTTCCTCCCTCCCCTGCCCTATGGCTCCATACCTAAGGATCCTAAAGCCCTGTGATAGTGGCCACCCATACCTCTGAGCATCATGGAATGCTCAAATCCAAGACCAGAGTGACAAGCCCCTCCATCCTTTCAAGATGGTGCTGAGGCAGTGTTGGACTAGGCTGAGCCCTATGGCTGCTGGGTCCTCCAGGGTAAGGGATGACCCCAGGAGGAGGCGGAGAGGTCAGACTGTTAGGCTTGGACCATGATAGATCTCCCGATGTCCTTCCAGCTATCTACTCTTGCACCCTCTAGGCAACCTGCTCTTCTCTCTTGATCACTTATCCCGCCCCCTCACTCCCCACTCAGCATGTTGGGAGGTGCCAGCCCCGTGGTGGTGGCCACTGTCCTTCAGTGTATCCAGATGCCTCTTCAGGAGTGATGAGGGCTTTACCTGCGAGGTGCTGGGGATGCGGCCAGCCATGCTTCCTGGGAAGAAGGCTGAAGATTGAGTCCCGTGTGGGAGCTTTTTATTTGGGGCTTTGGTTTTTCAAGGCAGGGTTTCTCTGTGTAGCCCTGGGTATCCTGGAACTCACTCTGTAGACCAGGCTGGCCTTGGAACTCACAGAGATCCATCTGTCTCTGCCTCCCAAATACTGGGATTAAAGGGCATGTACCATGCCACAGTGCGCTGAGCTTGGGAGCTTCTCTCTGGACTGTGGGGTATTAAGGGAGAACCAGTCAGGGTCCACCCTACCCCCACCCCACCCCTGTAGGCAACTTCTTTTCTGAAGGCCTGGGAGTAGCCTAGATGTTCAGGTGTGCTTTGGCATTGTTCTATCCCCTCAGGGTTTCCTTTCTTCTCTTAGGCAGAGAAGGTGCCTGGGGGTGGGAGAGGTTGGATGGGTAGTGACTCCCAGTACTCTGGCCACCCCTCTGTGCACACTAGTTAGGATGAGGAGTCCATTCCTTTATCTTCTTGTGGGTCTCTGCACACACCCTAGCCTTCCTCTCCACTTTTCTCCTCTTCCCTACCCCCTCCTTCCTCCTCCCCCACCTCTGAGTCAAAGAAGATCCCTCAGTTGTCACCATGGAAACCAAGATAGTGAAACTTTGGATGGGACCCTCCATCTCCGGAGGCTGCTTGCTGCAGGTATTGTCAAGGGTCGGGTGCCTCTGTATATGTTGGCCCATCACACTCCTCAG
Seq C2 exon
GGGAGGGCCTGCCCCAGCCCAGACTGGAAGAGGAGATCGATTCTCTGGCCCAGGAACTGGCACTGAAGGAGAAGGAGGCGGGGCACTCAAGGCTGACCGCACAGCCCTTGCTTGAGGCTGCGCAGAAGCTCCTGGAGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015094-Npdc1:NM_008721:2
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.097 A=NA C2=0.466
Domain overlap (PFAM):
C1:
PF068096=NPDC1=FE(14.4=100)
A:
NA
C2:
PF068096=NPDC1=FE(14.2=100)
Main Inclusion Isoform:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGCTACCACCTGTCCTGGAA
R:
CCAGGAGCTTCTGCGCAG
Band lengths:
282-1516
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: