HsaINT0115137 @ hg19
Intron Retention
Gene
ENSG00000107281 | NPDC1
Description
neural proliferation, differentiation and control, 1 [Source:HGNC Symbol;Acc:7899]
Coordinates
chr9:139935514-139937525:-
Coord C1 exon
chr9:139937379-139937525
Coord A exon
chr9:139935640-139937378
Coord C2 exon
chr9:139935514-139935639
Length
1739 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGA
5' ss Score
10.03
3' ss Seq
TGGCCCCTCACCCTCCCCAGGCG
3' ss Score
8.81
Exon sequences
Seq C1 exon
ATGTAGCCGCCTGTCCCGGGAGCCTGGACTGTGCCCTGAAGAGGCGGGCAAGGTGTCCTCCTGGTGCACATGCCTGTGGGCCCTGCCTTCAGCCCTTCCAGGAGGACCAGCAAGGGCTCTGTGTGCCCAGGATGCGCCGGCCTCCAG
Seq A exon
GTACGAGAGCAAAGGGGGAAGTCGATGGGGGGATGTCCCTGCATGAACCTCTCCCTGTAAGAAGCGGCCGGCTGGGCGCGGTGGCTCATGCCTGTAATCCCAGCACTGTGGGAGGCCCAGGCTGTTGGATCTCATGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAGTAGCCGGGTGTGGTGGCACACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTTAACCCGGGAGGCGGAGCTTGCAGTGAGCCGATTCACCACTGCACTCCAGCCTGGGCGACAGTGCGAGACTCTGTCTCAAAAAAAAAAAAAAAAAAAAAGAAGGCCGGGAGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCACATCATAAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATCTGTACTAAAAATACAAAAACAAAATTAGCCGGGCGTGGCGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAAGCTAAGGCAGGAGAATGGCGTGAACCCGGGAGGCAGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGGCAGAGCGAGACTCCGCCTCAAAAAAAAAAAAGCAGCAGCCTGCAGCCTCAATGCCCAGGCCTGTGCCAGGTGGTCTTGGGGCCCCTGGACCTTGTGGGGTGTTGGGTCCAAGGCCTGGGAGATCCTCATTCACTCTCCACGAAGCCTCCCATCCTTTCCAAATGGAGGTGGGCCCAGGCCTGGGGCAGTCAGGCCCTCCCAGGAGAAGGGCTGCACGATGTGAAATGCTGGGATGGCCACGGGAGAGGAAGGGCCCATTCTCCCCGGGCCTGGGCTCTGCAGGGTCTGCCCAGAAGCCCTCCAGGCCCCCACTTCCCCGTCCCCAGGCAGCTTGCTCTTTTCCACCACTCACTGTCCTGTCCGCCTGTTGGCAAATGTTGAAGGGTGCCAGCACTGGCTGGGTGCTGGGGATGCCCCGCTCGCCAGCCTGAGCCGCATCTGTCGGGATGGCCAGTCACTGAGTGACTTCAGGTGTGGTGAGGGCTTTGCTCAGAGGTGCTGGGGGTGGGAGCAGCAGCGGCTTCCTGGAGGAGGTGTTGAGAGGAGCACCGAGAAGTGGCTGTAAGGGTCTGTGTGGATGCACCTCCTGCCAACCTGGGAGCGTCCACCCAGACTGTGCAGCCCACAGTGGGTACCGGTGGAGCCCTGCCACCAGCCCCACCCCTGACAGCTGCCCCCGTTCTCCCAATGACCTGGGGAGGGGTCCCGGGTGCTTGGCTTCCTTCGGCTTCCCCCCACTCCTTGGGGAGTCCCTGCCCCTCTACCCGAGAAGGTGCTTGGAGGTGGGGAAGCAGAAGGGGCTGTGCTGGCCAGCCCTTTATGGACATGGGTTGGGGCGAGAGACCCCACTCCTTCCTCCCCGTGCCCGGTCTTTGGACGTTTCCCTAGCGCCTCCTCCCTTGCCCTGCCTCCACTTTCCGGGAAGCACTGCCCCTCACAGGAAGCGCCCGCGCTGTCACCATGGCAATCTGGGAGGGAGAGGGCCTCCAGGCGTGTACCCAGTCCTCAGGCTCCTGGGAGGAACCTGCCAGAAGCGGGGAGGCCGGGCCTGGGGCTACCTCCTGGACGGACCCCTCCACCTGATGGCCCCTCACCCTCCCCAG
Seq C2 exon
GCGGGGGCCGGCCCCAGCCCAGACTGGAAGATGAGATTGACTTCCTGGCCCAGGAGCTTGCCCGGAAGGAGTCTGGACACTCAACTCCGCCCCTACCCAAGGACCGACAGCGGCTCCCGGAGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107281-NPDC1:NM_015392:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.432 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF068096=NPDC1=PU(22.9=43.0)
A:
NA
C2:
PF068096=NPDC1=FE(13.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGTAGCCGCCTGTCCCG
R:
CTGTCGGTCCTTGGGTAGGG
Band lengths:
257-1996
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)