HsaINT0025666 @ hg19
Intron Retention
Gene
ENSG00000198870 | C9orf96
Description
chromosome 9 open reading frame 96 [Source:HGNC Symbol;Acc:28669]
Coordinates
chr9:136259418-136260890:+
Coord C1 exon
chr9:136259418-136259536
Coord A exon
chr9:136259537-136260726
Coord C2 exon
chr9:136260727-136260890
Length
1190 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGC
5' ss Score
4.72
3' ss Seq
GCTGTCCTCTCTCCGTGCAGGGC
3' ss Score
11.4
Exon sequences
Seq C1 exon
ACCCCTTTCGTAAGTCCTGGATGGCCCCTGAAGCCCTCAACTTCTCCTTCAGCCAGAAATCAGACATCTGGTCCCTGGGCTGCATCATTCTGGACATGACCAGCTGCTCCTTCATGGAT
Seq A exon
GTGAGCCGCCCTCCCTCCCCCACACCCCACATGCTGTTCCCCACGCGCCCAGGCCTGGGGAAAAGGCTTGGCCTCACCCTGCCTCCCCTCTGCATCCCTTCCCCTGGCTCTCTGCAGGCTGCACAGAGCCCTCTTCTCCACCTGCGAGGGGCCTGCCCTCCTCAGAACCCCTCAGCTTGCAGCACCTGCTGGGCTCTAGCAGGATAATGACAGCAGTGGTAATATTCAGACCATCCCACGCGACCCTCGCAGCAGCCCTCCAGGTGGTGTCACTGACTCTTGATGGAGAAAAGCCAAGTTCAGGTGCCCTTGTGAGCATGAAGGCTGCACGGAGTTGCAAGCAACGGGAACCCAGTGTGGGCCTGAACACACCTGGCTGTCTCATGCACAAGCCCCAGGCTGGTGTGGAGGTGCCTTCTCTCCTCCTGCACATCCTTAGCATGCAGCTCTTTCTCTCATCCCTGCTGGGGCCCCTGCACCATGGCCACAGCCTGTGGGCAGGAAGGAGGGGAGGCAGAGGGCCCCACTGGCCCCGCGAGCACTCCAAGGTCACTCTGGCTGCAGGGAGGCAGGGAAGTCCAGCCTGTCGCTTCCTATCCTCTATATGCAGAAGAGAAAAGTGGGGAAGGCCTGCCATGCCCAAAACAAGGAAGCTCCCCTTCTCCGCAGCACCACCTGCAGGCACCGAGGTCCCCAGAAAGGACAGACACCTGGCTGGACCCAGGTTCCCCATGGTCTCCCAGACCCCCAGACTCCACCTCTGAGAAGCACCTTGCCACTCCCTTCCTTTGAAAGACTCCCAGGGAAATGAGAGCCTTCCCACTTCGGAGGCTGTGTGACATCCTGGAAATTAGCCTGAGCTCCAGCCCCAGCCCAGGCAGTGTGACCCTGGGCATGCTCACACTCTGTGAAATGGGCATGCTGTCTTACTGGCTGGGTCTAGATCAGGGGGCTTTCTTGGCAGGACTCCACCCCGGGAGACAACCCGCTGGCTTCTCTGAAACTCCATTTCTTCTTATGGAAGAGCTTGGGGCCCCTGGGGTCTCTGGGCATTCTTGTAGACGGTGGCCACACCTGGCTCTCCCTGGTCTCCTCCTGGATTTCTTGGTCCCTGGTCGTCCCCTGCCCATGCTGGGACCTAGTTTTCATTTACTTAAGGGAATACACAGAGCTGTCCTCTCTCCGTGCAG
Seq C2 exon
GGCACAGAAGCCATGCATCTGCGGAAGTCCCTCCGCCAGAGCCCAGGCAGCCTGAAGGCCGTCCTGAAGACAATGGAGGAGAAGCAGATCCCGGATGTGGAAACCTTCAGGAATCTTCTGCCCTTGATGCTCCAGATCGACCCCTCGGATCGAATAACGATAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198870-C9orf96:NM_153710:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=FE(14.4=100)
A:
NA
C2:
PF0006920=Pkinase=FE(20.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
ACCCCTTTCGTAAGTCCTGGA
R:
TCGTTATTCGATCCGAGGGGT
Band lengths:
279-1469
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)