HsaINT0116386 @ hg19
Intron Retention
Gene
ENSG00000162068 | NTN3
Description
netrin 3 [Source:HGNC Symbol;Acc:8030]
Coordinates
chr16:2521500-2522890:+
Coord C1 exon
chr16:2521500-2522630
Coord A exon
chr16:2522631-2522701
Coord C2 exon
chr16:2522702-2522890
Length
71 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGG
5' ss Score
8.99
3' ss Seq
TGACCCATCCCTCCCTGCAGCTT
3' ss Score
10.19
Exon sequences
Seq C1 exon
GAGGACGCGCCAACATCCCCGCTGCTGTGCTGGGCCCGGGGCGTGCCCGCCGCTGCTCCCACCTCTGGGCCGGGCTGGGGCCGCCCGGGGGCCCTGTTCCTCGGCATTGCGGGCCTGGTGGGCAGAGCCGCGGAGAGGGCTTCTTTTCCCCAAGGGCAGCGTCTTGGGGCCCGGCCACTGGCTGACCCGCAGCGGCTCCGGCCATGCCTGGCTGGCCCTGGGGGCTGCTGCTGACGGCAGGCACGCTCTTCGCCGCCCTGAGTCCTGGGCCGCCGGCGCCCGCCGACCCCTGCCACGATGAGGGGGGTGCGCCCCGCGGCTGCGTGCCAGGACTGGTGAACGCCGCCCTGGGCCGCGAGGTGCTGGCTTCCAGCACGTGCGGGCGGCCGGCCACTCGGGCCTGCGACGCCTCCGACCCGCGACGGGCACACTCCCCCGCCCTCCTTACTTCCCCAGGGGGCACGGCCAGCCCTCTGTGCTGGCGCTCGGAGTCCCTGCCTCGGGCGCCCCTCAACGTGACTCTCACGGTGCCCCTGGGCAAGGCTTTTGAGCTGGTCTTCGTGAGCCTGCGCTTCTGCTCAGCTCCCCCAGCCTCCGTGGCCCTGCTCAAGTCTCAGGACCATGGCCGCAGCTGGGCCCCGCTGGGCTTCTTCTCCTCCCACTGTGACCTGGACTATGGCCGTCTGCCTGCCCCTGCCAATGGCCCAGCTGGCCCAGGGCCTGAGGCCCTGTGCTTCCCCGCACCCCTGGCCCAGCCTGATGGCAGCGGCCTTCTGGCCTTCAGCATGCAGGACAGCAGCCCCCCAGGCCTGGACCTGGACAGCAGCCCAGTGCTCCAAGACTGGGTGACCGCCACCGACGTCCGTGTAGTGCTCACAAGGCCTAGCACGGCAGGTGACCCCAGGGACATGGAGGCCGTCGTCCCTTACTCCTACGCAGCCACCGACCTCCAGGTGGGCGGGCGCTGCAAGTGCAATGGACATGCCTCACGGTGCCTGCTGGACACACAGGGCCACCTGATCTGCGACTGTCGGCATGGCACCGAGGGCCCTGACTGCGGCCGCTGCAAGCCCTTCTACTGCGACAGGCCATGGCAGCGGGCCACTGCCCGGGAATCCCACGCCTGCCTCG
Seq A exon
GTGAGGCCTTGGAGGGTGGCCTGGGGACCTTGGACACAACCAGCCTGCCCCTGACCCATCCCTCCCTGCAG
Seq C2 exon
CTTGCTCCTGCAACGGCCATGCCCGCCGCTGCCGCTTCAACATGGAGCTGTACCGACTGTCCGGCCGCCGCAGCGGGGGTGTCTGTCTCAACTGCCGGCACAACACCGCCGGCCGCCACTGCCACTACTGCCGGGAGGGCTTCTATCGAGACCCTGGCCGTGCCCTGAGTGACCGTCGGGCTTGCAGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162068-NTN3:NM_006181:1
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=0.171 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
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACCTGATCTGCGACTGTCG
R:
ACAGTCGGTACAGCTCCATGT
Band lengths:
178-249
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)