HsaINT0116390 @ hg19
Intron Retention
Gene
ENSG00000162068 | NTN3
Description
netrin 3 [Source:HGNC Symbol;Acc:8030]
Coordinates
chr16:2523430-2524146:+
Coord C1 exon
chr16:2523430-2523504
Coord A exon
chr16:2523505-2523756
Coord C2 exon
chr16:2523757-2524146
Length
252 bp
Sequences
Splice sites
5' ss Seq
ATGGTAGGT
5' ss Score
8.6
3' ss Seq
CCCTCTCGCTCTCCCCGCAGCGG
3' ss Score
13.47
Exon sequences
Seq C1 exon
ACTGTGACTCGCACTGCAAACCTGCCCGTGGCAGCTACCGCATCAGCCTAAAGAAGTTCTGCAAGAAGGACTATG
Seq A exon
GTAGGTGCCCTCAGGCCTCCCGCGGACCTTCCCACCTTCCTCCTCTCCCTACCTTCCCTCCTCCGCCAGCTTCCCCTTGGAACGCCTTGACCCTTGCTGGGCCCCAAGGCCCATCCTCATCCCTCAGGTCCTCCACGGGCAGCGACCCCGCCCCTTCAGCCCCCACTGCCCTCCTGGTGTCCTCCCCGTGCCTCCCCCTACCGCGGGCAGGCCGCCCCTTCCTGACCCCGCCCCCTCTCGCTCTCCCCGCAG
Seq C2 exon
CGGTGCAGGTGGCGGTGGGTGCGCGCGGCGAGGCGCGCGGCGCGTGGACACGCTTCCCGGTGGCGGTGCTCGCCGTGTTCCGGAGCGGAGAGGAGCGCGCGCGGCGCGGGAGTAGCGCGCTGTGGGTGCCCGCCGGGGATGCGGCCTGCGGCTGCCCGCGCCTGCTCCCCGGCCGCCGCTACCTCCTGCTGGGGGGCGGGCCTGGAGCCGCGGCTGGGGGCGCGGGGGGCCGGGGGCCCGGGCTCATCGCCGCCCGCGGAAGCCTCGTGCTACCCTGGAGGGACGCGTGGACGCGGCGCCTGCGGAGGCTGCAGCGACGCGAACGGCGGGGGCGCTGCAGCGCCGCCTGAGCCCGCCGGCTGGGCAGGGCGGCCGCTGCTCCCACATCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162068-NTN3:NM_006181:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.017
Domain overlap (PFAM):
C1:
PF0175916=NTR=PU(7.0=30.8)
A:
NA
C2:
PF0175916=NTR=PD(92.1=89.7)
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:
AAGAAGTTCTGCAAGAAGGACT
R:
CCTCCAGGGTAGCACGAGG
Band lengths:
306-558
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)