MmuINT0111254 @ mm9
Intron Retention
Gene
ENSMUSG00000079662 | Ntn3
Description
netrin 3 [Source:MGI Symbol;Acc:MGI:1341188]
Coordinates
chr17:24344744-24346332:-
Coord C1 exon
chr17:24345004-24346332
Coord A exon
chr17:24344933-24345003
Coord C2 exon
chr17:24344744-24344932
Length
71 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGG
5' ss Score
6.9
3' ss Seq
TGACTGACCCTTCCCTGCAGCTT
3' ss Score
9.96
Exon sequences
Seq C1 exon
CTCGCTGCAGCCAGGAGAAGCCGGCAGCCCGGGCGCCCCAGGCCCCGCCCGCCCAAGGCCCTTCCCGGGAGGCCGGGAGACCTGCTCCTCCTGGCCCTCCGTGGGTGAGTGCTGGCGGCCGGCGGCGGGTGGGGCCTCCGCGGGCGGAGGCACCGGGAGCGGGGGCGACGCCTGTCAACGCTTCAGGCCTAGCAGGAGGACTCGCCAACATCCCTGCTCCTGTGCTCGGCCCCGGGCGTGCCGGTGGCTGCTCCCACTTCTGGGCCTGTGCTGGGGGCCGCCCTGGTGCTCTGCTATCTTGGCACTGCAGACCCGGCACGCAGAGTAGCGGACTAGGCTCTCTCTTCGAGGGCAGACTCGTTAGGCGGAAGCTGGCTGGTTGACTTACAGCGGCCACGGCCATGCCCACCTGGCTCTGGGGGCTGCTGCTGACCGCGGGCACGCTCTCCGCTGCACTGAGCCCAGGGCTGCCGGCCTCTGCCGACCCCTGCTATGATGAGGCGAGGGAGCCTCGCTCTTGTATTCCTGGCCTTGTGAACGCTGCTCTGGGCCGAGAGGTGCTGGCGTCCAGCACGTGCGGGAGGTCGGCCAATCGCGTCTGCGATTCCTCGGACCCGCAGCGGGCACACTCTGCAGACCTCCTGACCTCTGCTCCGGGCACTGCAAGTCCTCTCTGTTGGCGCTCCGATTTGCTGCAACAGGCACCTTTCAACGTAACCCTCACAGTGCCCCTGGGGAAGGCTTTTGAGCTGGTCTTCGTGAGCCTGCGCTTCTGCTCAGCTCCTCCAACCTCCGTGGCCCTGCTTAAGTCGCAGGACCATGGCCGCAGCTGGGTCCCCTTGGGCTTCTTCTCTTCCAGCTGTACCCTGGACTATGGCCGTCTGCCTGCTCCTGCTGATGGCCCTTCTGGTCCAGGGCCAGAAGCCCTCTGCTTTCCAGCCCCCCAGGCTCAGCCTGATGGTGGAGGCCTTCTGGCCTTCAGTGTGCAGGATGGCAGCCCACAGGGCCTGGATCTGGACAACAGCCCCGTGCTCCAAGACTGGGTGACTGCCACAGATATTCGCATAGTACTCACAAGGCCTGCCATTCAGGGAGACACCAGGGACGGTGGGGTGACAGTCCCCTACTCCTACTCAGCCACTGAGCTTCAGGTGGGAGGTCGATGCAAGTGCAATGGGCATGCCTCACGGTGTCTGTTGGACACCCATGGCCACCTGGTCTGCGACTGCCAGCATGGTACAGAGGGCCCTGATTGCAGCCGCTGCAAGCCCTTCTACTGCGACAGGCCATGGCAGCGGGCTACAGGGCAGGAAGCCCACGCTTGCCTTG
Seq A exon
GTGAGGCCTTGGAGGGTAGCCTGGGGACTTCTGACCAGGCAGGGCTGCCCCTGACTGACCCTTCCCTGCAG
Seq C2 exon
CTTGCTCCTGCAACGGCCATGCGCGAAGATGCCGCTTCAACATGGAGCTCTACCGACTGTCCGGCCGCCGCAGTGGGGGCGTGTGCCTCAACTGCCGGCACAATACAGCTGGTCGTCACTGCCACTACTGCCGGGAGGGCTTCTATCGTGATCCAGGCCGTGTCCTGAGTGACCGTCGTGCTTGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079662-Ntn3:NM_010947:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.097 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005512=Laminin_N=WD(100=69.0),PF0005319=Laminin_EGF=WD(100=17.4)
A:
NA
C2:
PF0005319=Laminin_EGF=WD(100=95.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAGCCCTTCTACTGCGACAG
R:
TGACGACCAGCTGTATTGTGC
Band lengths:
183-254
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: