HsaINT0115142 @ hg19
Intron Retention
Gene
ENSG00000107281 | NPDC1
Description
neural proliferation, differentiation and control, 1 [Source:HGNC Symbol;Acc:7899]
Coordinates
chr9:139934423-139934888:-
Coord C1 exon
chr9:139934809-139934888
Coord A exon
chr9:139934520-139934808
Coord C2 exon
chr9:139934423-139934519
Length
289 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGT
5' ss Score
10.49
3' ss Seq
AGCGATCCCCCCCCACCCAGGCA
3' ss Score
5.62
Exon sequences
Seq C1 exon
CCTGGGGACCAGCGGCTGGCACAGAGCGCGGAGATGTACCACTACCAGCACCAACGGCAACAGATGCTGTGCCTGGAGCG
Seq A exon
GTGAGTGGCCGCCCCGGCACTGCCACCCCCACCCACCCACCCCCCATCCCCACCTCCACCTCCATTTCCACCTCCCCTGGCCAACTTTACCCCAGGCCCTGCCACCCTCACCTGCACGCTAACCTTCACCTCCCCCGCCGCCCTGCACCCTCACCTCCCCTGGCCAACTTCACCCTGGGCTGTGCTCCCCTGCCACCCCAGGGCTGAGGTGGGCTGAGTGCCCACTTCCAGACTGGGCCACTGGCACCTCGAGGGCATGGGGAGGACCCAGCGATCCCCCCCCACCCAG
Seq C2 exon
GCATAAAGAGCCACCCAAGGAGCTGGACACGGCCTCCTCGGATGAGGAGAATGAGGACGGAGACTTCACGGTGTACGAGTGCCCGGGCCTGGCCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107281-NPDC1:NM_015392:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.741 A=NA C2=0.848
Domain overlap (PFAM):
C1:
PF068096=NPDC1=FE(8.4=100)
A:
NA
C2:
PF068096=NPDC1=FE(10.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACAGAGCGCGGAGATGTAC
R:
CCCGGGCACTCGTACACC
Band lengths:
148-437
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)