HsaINT0025362 @ hg38
Intron Retention
Gene
ENSG00000148362 | C9orf142
Description
chromosome 9 open reading frame 142 [Source:HGNC Symbol;Acc:HGNC:27849]
Coordinates
chr9:136993053-136993664:+
Coord C1 exon
chr9:136993053-136993243
Coord A exon
chr9:136993244-136993579
Coord C2 exon
chr9:136993580-136993664
Length
336 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
CCTGTCCTGTTTTCCCCCAGACC
3' ss Score
12.89
Exon sequences
Seq C1 exon
GGCAGCCTGTGAGCAGCAAGCTGTGGCTCTGACTCTGCAGGAGGACAGAGCATCCCTGACGCTTTCAGGGGGGCCCTCGGCACTGGCCTTTGACCTCTCCAAGGTACCAGGCCCAGAGGCAGCCCCCAGGCTGCGGGCGCTGACACTGGGCCTGGCAAAACGCGTGTGGAGCCTGGAGCGGCGACTGGCAG
Seq A exon
GTAGGATTGGGGGTGGGCACCTCATACCTTCACTGGGGTCCCCTGCTCTTGCCCCCACTCCTGGCACTGAGTGGGGTTCCCATGGGCTTTCCTCCCCAGCTGCAGAAGAGACAGCTGTCAGCCCGAGGAAGAGCCCCCGGCCTGCAGGGCCTCAGCTCTTCTTACCAGGTAAGGCATGTCCGCCTGTGACTCAAGTAGGGCTGTGCTCTTTAACCTGGAACTCAGTTTCCCCCCAAACAAGACTCACGCTCCAGAGAGAATGCCTATCTATTCGGAGAAGGTTGTGGTTGGGATGCTGCCAGGTTCAGGAGCTGCCCCTGTCCTGTTTTCCCCCAG
Seq C2 exon
ACCCAGATCCCCAGAGAGGTGGCCCTGGACCTGGAGTCAGGAGGCGGTGTCCAGGAGAGTCGCTCATCAACCCCGGGTTCAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148362:ENST00000492564:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.108 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF153841=DUF4610=FE(32.3=100)
A:
NA
C2:
PF153841=DUF4610=FE(14.1=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
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:
CAGCCTGTGAGCAGCAAGC
R:
CTTGAACCCGGGGTTGATGAG
Band lengths:
272-608
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