HsaINT0025363 @ hg19
Intron Retention
Gene
ENSG00000148362 | C9orf142
Description
chromosome 9 open reading frame 142 [Source:HGNC Symbol;Acc:27849]
Coordinates
chr9:139887795-139888116:+
Coord C1 exon
chr9:139887795-139887863
Coord A exon
chr9:139887864-139888031
Coord C2 exon
chr9:139888032-139888116
Length
168 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
CCTGTCCTGTTTTCCCCCAGACC
3' ss Score
12.89
Exon sequences
Seq C1 exon
CTGCAGAAGAGACAGCTGTCAGCCCGAGGAAGAGCCCCCGGCCTGCAGGGCCTCAGCTCTTCTTACCAG
Seq A exon
GTAAGGCATGTCCGCCTGTGACTCAAGTAGGGCTGTGCTCTTTAACCTGGAACTCAGTTTCCCCCCAAACAAGACTCACGCTCCAGAGAGAATGCCTATCTATTCGGAGAAGGTTGTGGTTGGGATGCTGCCAGGTTCAGGAGCTGCCCCTGTCCTGTTTTCCCCCAG
Seq C2 exon
ACCCAGATCCCCAGAGAGGTGGCCCTGGACCTGGAGTCAGGAGGCGGTGTCCAGGAGAGTCGCTCATCAACCCCGGGTTCAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148362-C9orf142:NM_183241:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.917 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF153841=DUF4610=FE(11.6=100)
A:
NA
C2:
PF153841=DUF4610=FE(14.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCAGAAGAGACAGCTGTC
R:
CTCTTGAACCCGGGGTTGATG
Band lengths:
154-322
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)