HsaINT0110809 @ hg19
Intron Retention
Gene
ENSG00000130287 | NCAN
Description
neurocan [Source:HGNC Symbol;Acc:2465]
Coordinates
chr19:19334830-19335242:+
Coord C1 exon
chr19:19334830-19335004
Coord A exon
chr19:19335005-19335114
Coord C2 exon
chr19:19335115-19335242
Length
110 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGG
5' ss Score
8.99
3' ss Seq
CCCTCCCCTTGTGTTGTCAGGTA
3' ss Score
9.51
Exon sequences
Seq C1 exon
GTGTTGTGTTCCACTACCGATCAGCCCGGGACCGCTATGCACTGACCTTCGCTGAGGCCCAGGAGGCCTGCCGTCTCAGCTCAGCCATCATTGCAGCCCCTCGGCATCTACAGGCTGCCTTTGAGGATGGCTTTGACAACTGTGATGCTGGCTGGCTCTCTGACCGCACTGTTCG
Seq A exon
GTGAGGGGGATACACAGGGCAGGGAGATGAAGACTAGCTCATGGGGAAGGAGGTTCCTTGGGGGCTCCAGGAGCACACATCTGAGAGGGACCCTCCCCTTGTGTTGTCAG
Seq C2 exon
GTATCCTATCACCCAGTCCCGTCCTGGTTGCTATGGCGACCGTAGCAGCCTTCCAGGGGTTCGGAGCTATGGGAGGCGCAACCCACAGGAACTCTACGATGTGTATTGCTTTGCCCGGGAGCTGGGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130287-NCAN:NM_004386:4
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=0.000
Domain overlap (PFAM):
C1:
PF0019312=Xlink=PU(60.4=98.3)
A:
NA
C2:
PF0019312=Xlink=PD(38.5=84.1),PF0019312=Xlink=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACCGCTATGCACTGACCTTC
R:
GTAGAGTTCCTGTGGGTTGCG
Band lengths:
243-353
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)