HsaINT0025361 @ hg38
Intron Retention
Gene
ENSG00000148362 | C9orf142
Description
chromosome 9 open reading frame 142 [Source:HGNC Symbol;Acc:HGNC:27849]
Coordinates
chr9:136992761-136993243:+
Coord C1 exon
chr9:136992761-136992974
Coord A exon
chr9:136992975-136993052
Coord C2 exon
chr9:136993053-136993243
Length
78 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CCGCACCTCTCCTCTCCCAGGGC
3' ss Score
9.08
Exon sequences
Seq C1 exon
GGGGCGACAGACATCTGGGATTCCCCAGAAGGCTCTGACACCCTCTGCCCGCCCTGTAGCTGTAGTCCTCCCATTGGCTAGGGCTCTGGGGTCGGGCAGGTTTCGGGTGCCCCCAGTGGGCCTCGGGTTCCAGGCAGCTCGTGACAAGCCCCTGTGCTCTCTAGAAAGCCCGTTTTGGCCTGAGTGCGGCTGAGGACATCACCCCCCGGTTCAG
Seq A exon
GTGAGACCCAAGCAGGGAGGAAGGACGGGTGGGGAGGAGGAGGGTCTGCCACAGCTCTCCGCACCTCTCCTCTCCCAG
Seq C2 exon
GGCAGCCTGTGAGCAGCAAGCTGTGGCTCTGACTCTGCAGGAGGACAGAGCATCCCTGACGCTTTCAGGGGGGCCCTCGGCACTGGCCTTTGACCTCTCCAAGGTACCAGGCCCAGAGGCAGCCCCCAGGCTGCGGGCGCTGACACTGGGCCTGGCAAAACGCGTGTGGAGCCTGGAGCGGCGACTGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148362:ENST00000492564:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.108
Domain overlap (PFAM):
C1:
PF153841=DUF4610=FE(8.1=100)
A:
NA
C2:
PF153841=DUF4610=FE(32.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAGCCCCTGTGCTCTCTAGA
R:
TTGGAGAGGTCAAAGGCCAGT
Band lengths:
172-250
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