HsaINT0025362 @ hg19
Intron Retention
Gene
ENSG00000148362 | C9orf142
Description
chromosome 9 open reading frame 142 [Source:HGNC Symbol;Acc:27849]
Coordinates
chr9:139887505-139887863:+
Coord C1 exon
chr9:139887505-139887695
Coord A exon
chr9:139887696-139887794
Coord C2 exon
chr9:139887795-139887863
Length
99 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
CCATGGGCTTTCCTCCCCAGCTG
3' ss Score
8.45
Exon sequences
Seq C1 exon
GGCAGCCTGTGAGCAGCAAGCTGTGGCTCTGACTCTGCAGGAGGACAGAGCATCCCTGACGCTTTCAGGGGGGCCCTCGGCACTGGCCTTTGACCTCTCCAAGGTACCAGGCCCAGAGGCAGCCCCCAGGCTGCGGGCGCTGACACTGGGCCTGGCAAAACGCGTGTGGAGCCTGGAGCGGCGACTGGCAG
Seq A exon
GTAGGATTGGGGGTGGGCACCTCATACCTTCACTGGGGTCCCCTGCTCTTGCCCCCACTCCTGGCACTGAGTGGGGTTCCCATGGGCTTTCCTCCCCAG
Seq C2 exon
CTGCAGAAGAGACAGCTGTCAGCCCGAGGAAGAGCCCCCGGCCTGCAGGGCCTCAGCTCTTCTTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148362-C9orf142:NM_183241:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.108 A=NA C2=0.917
Domain overlap (PFAM):
C1:
PF153841=DUF4610=FE(32.3=100)
A:
NA
C2:
PF153841=DUF4610=FE(11.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTGGCCTTTGACCTCTCCAA
R:
GGTAAGAAGAGCTGAGGCCCT
Band lengths:
177-276
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)