HsaINT0025606 @ hg19
Intron Retention
Gene
ENSG00000165698 | C9orf9
Description
chromosome 9 open reading frame 9 [Source:HGNC Symbol;Acc:1367]
Coordinates
chr9:135763677-135765418:+
Coord C1 exon
chr9:135763677-135763824
Coord A exon
chr9:135763825-135765343
Coord C2 exon
chr9:135765344-135765418
Length
1519 bp
Sequences
Splice sites
5' ss Seq
CACGTGAGT
5' ss Score
9.3
3' ss Seq
GTTGGTTTTTCCCTTCACAGGGG
3' ss Score
9.07
Exon sequences
Seq C1 exon
ATACCCTCATGATGTGGTGAACCACCTCAGCTGTGACGAGGCCCGGAACCACTACGGCGGCGTGGTCAGCCTCATCCCCCTCATCCTAGACTTAATGAAAGAATGGATCGCCCACTCCGAGAAGTTGCCGCGCAAGGTGCTGCAGCAC
Seq A exon
GTGAGTGAGCCCCAGGCGCACCAGGAGAGCACCAGGGGAGCCGCTCGTCCTGCCCAGGCCATAGGGACCCAGCCCAGGGCCACTAAACACAAGTGTAGACAGCTCACAAAAGCCAGCCTCAAACCCAGGGGATGTTCAAAACCACCCTGGAGGCCTCCTGGTGGGAAATTGTAACTCAGAGCCAGGAGCTCCGTCGGCGGAGAGCTTTGCTGTTTAATTTGGATTTTACTGGTTGGTCCTTTTTTCACTGGTACCCATGGACCCTGCCACTTACTAACCCCAAGGGAATCAGCCAATATATTACTGAGACTTCCTCTCTCTCTTCTTGCTTTAACTTCTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCGGTGGCGCAACCTCGGCTCACTGCAACCTCCGCCTCCCAGGTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCGCCCACCACCTCGCCTGGCTAATTTTTTGTATTTTTAGTAGAGACAGCGTTTCACCATGTTAGCCAGGATGGTCTCAATCTCCTGACCTCATGATCTACCCTCGTGATCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACAGCGCCCGGCCCTCTTGCTTTAACTTCTAACATTTCCACTTCTAAGCATCAGGCTCCGTGCTGATGAAGAGGAAACCCACTTACAGAAGTTGCCCAAACAGGATGGTGTGGTAGAGGGTCCCAGGAGGGCACTGAACTGTCACCTAGGTCCTCTTTGAGCCACATCCGGCTCCAGTGCCACGCCTGTCCCTGCTGCGGGCTGCAGTTTTGCAGAGGGTGATCAAGCTGGAGACCATCTGCTCCTTGCCCCACCACCAGCCCCAACTGTAGGCAAGGCACACGCTGTTTGCGAGCCAGGGATGCTCCCCTCCAGGATGGAGTGGGGGTCGGCATGTGGAACTCAGCGTGTTTATTTTTTTATTTTTTGAGATGGAGTTTCACTCTGTCTCCCAGGCTGGAGTGCAGTGGCACGATCTTGGCTCACTGCAACCTCCACCTCCAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGAATTACAGGCGCCCACCACCCCACCTGGCTAATTTATATATATATATATTTTTTAGTAGAGACGGGGCTTCACCACGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCAACTGGTCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACGGCACCTGGCCAGAACTCAGTAGTGTGTTTAGTTCTCTGGACCACAGCCAAAGGGGAATAAACTCACCTTTCCTTCGCCTTTACTTGGGAGAGGGAGACCATGACAGAAGCCAGAATTCTGATTTTGTGGCTCCTGAGCAAGGGCGATGACCTGGTTTTCACAGCGTAGTCGAACCCCAAACATTGTAAAATGTGTCCCTGGCTTCTGAGCTTGCCCAAAGTAATGTCTGACTGTTGGTTTTTCCCTTCACAG
Seq C2 exon
GGGACGACTTAGCTTCTGTATTATTGTTGCTTCCTCAGGGGGAGACAGTCAAGAATAAAAAGTATTCTACCACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165698-C9orf9:NM_018956:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.272 A=NA C2=0.555
Domain overlap (PFAM):
C1:
PF151201=DUF4561=PD(32.6=51.9)
A:
NA
C2:
PF151201=DUF4561=PD(0.6=25.0)
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:
ACCCTCATGATGTGGTGAACC
R:
TTTTATTCTTGACTGTCTCCCCCTG
Band lengths:
206-1725
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)