HsaINT0116387 @ hg19
Intron Retention
Gene
ENSG00000162068 | NTN3
Description
netrin 3 [Source:HGNC Symbol;Acc:8030]
Coordinates
chr16:2522702-2523135:+
Coord C1 exon
chr16:2522702-2522890
Coord A exon
chr16:2522891-2522985
Coord C2 exon
chr16:2522986-2523135
Length
95 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGC
5' ss Score
5.97
3' ss Seq
CTTCCCACCTCTGTCCTCAGCCT
3' ss Score
8.55
Exon sequences
Seq C1 exon
CTTGCTCCTGCAACGGCCATGCCCGCCGCTGCCGCTTCAACATGGAGCTGTACCGACTGTCCGGCCGCCGCAGCGGGGGTGTCTGTCTCAACTGCCGGCACAACACCGCCGGCCGCCACTGCCACTACTGCCGGGAGGGCTTCTATCGAGACCCTGGCCGTGCCCTGAGTGACCGTCGGGCTTGCAGGG
Seq A exon
GTGAGCCACCACCGGCCACCTGCAGGCCCTCACCCTCTGACTTCCCAGATCCCCAGACAGGCTTCTGACCAGGCCCTTCCCACCTCTGTCCTCAG
Seq C2 exon
CCTGCGACTGTCACCCGGTTGGTGCTGCTGGCAAGACCTGCAACCAGACCACAGGCCAGTGTCCCTGCAAGGATGGCGTCACTGGCCTCACCTGCAACCGCTGCGCGCCTGGCTTCCAGCAAAGCCGCTCCCCAGTGGCGCCCTGTGTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162068-NTN3:NM_006181:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.039
Domain overlap (PFAM):
C1:
PF0005319=Laminin_EGF=WD(100=95.3)
A:
NA
C2:
PF0005319=Laminin_EGF=WD(100=94.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGGGGTGTCTGTCTCAACT
R:
GTGGTCTGGTTGCAGGTCTTG
Band lengths:
168-263
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)