HsaINT0025310 @ hg19
Intron Retention
Gene
ENSG00000198917 | C9orf114
Description
chromosome 9 open reading frame 114 [Source:HGNC Symbol;Acc:26933]
Coordinates
chr9:131589311-131591139:-
Coord C1 exon
chr9:131591014-131591139
Coord A exon
chr9:131589471-131591013
Coord C2 exon
chr9:131589311-131589470
Length
1543 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGC
5' ss Score
8.02
3' ss Seq
AACATCCCTCCCCTGCTCAGGGC
3' ss Score
8.45
Exon sequences
Seq C1 exon
AGAAAGAGGAGAAAAAAAAATGGAAGGATCTCAAGCTGATGAAAAAACTGGAGCGGCAGCGGGCACAGGAGGAACAGGCAAAGCGCCTGGAAGAGGAGGAGGCAGCGGCAGAGAAGGAGGACCGCG
Seq A exon
GTGAGCTGGGGTCTTGGGGAGGGCCACAGGTTGTGGCCCACGGTAGTTGTCCTGCAGGCAGAGCAGAGATGTCTTATCTGAAAGGGCCTTTACAGACCAGTAGGTCCAAACATCTTGTCCTGATGGAGAAACTGAGGCCCAGAGAAGGGAGGGAGCCAGCAAACTGAGTTCTGACCTCCTGCTTAGGTAAATTTCAAGCCTATGGAAGGCAAGCCTTATCTCTCTTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAACGGCGCCATCTCTGCTCACTGCAACCTCCACTGCCCAAGTTCAAGCAATTTTCCTCCCTCGGCCCCCCGAGTAGTTGGGATTACAGAAGTGTGCCACCACACCTGGCTAATTTTCGTATTTTTAGTAGAGACGTGGTTGCACCATGTTGGGGAGGCCGGTCTCGAACTCCTGACCTCAGGTGATCTGCCCACTTCAGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCGTGCCCGGCCCAAGCCTCATATCTCTTAACTTAGACCTCTAGAACTTCATGATCTTCCTGATTTTTTGACTTTTTTATTGAGCATTTTCTGTGTGCTTTAATTTCATTTTTCAATTATTTTGATTTCATAATAAAAATGAAAGAAAACTACAAAGAAGACAGGAACAATCCCAGCAAACATTGTAGCAAAAGCTTGTCCAAACAATTATAGCTACTTATCCATGTGTAGCAAAGTACAGATACAATGTTACAACAGTGAAACCATGTTATCTATGTGCTTCTTGGGCTTTTTTGTTTGTTTTTGAGACACAGTCTCGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCTCGATCTCCGCTCACTGCAATCTCCACTTCCCAGTTCAATCGATTCTCCTGCCCCAGCCTCCGGAGTAGCTGGGATTACAGGCATGCGCCACCATGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCGCCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCACTCAGGTGATCCGCCCGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCTTTTGTGTGACCTTGGGCCATGTATTTGACTTCCCGGGGCTGAAGGCCCCTGGTCTGTAAATGGGGATAATGGCAGTATCCTCACTAGGGATCAGGTTAATGGCTATCGGGTTAATGTGCACACACTAAAGACTTATTAGATATCAGCTTTCATTTTATCCCCATTTGATAGCTGGAGAACTGAGGCAGTAAGTGGGAGAGCCAGGATGTGAACTTAGGCCATTGCTACTAACCGCTCCACAGCCTCGCCCAGTGGTTTGCCCTGCTCAGAGGAGCCATGGAGACTGCTGGGAGACTGAGGCCCAGAGAGGGGAGCTGGATCTATTTTGCTCATCTCAAAATTCCTCCCACTTGGGAAATTCTCAAACCATGGGCGCTAGGGACAGAGGAAGGGAGAGAAAGGTAGGGGGCCCTTGCCTCTCACACTGGCTGGGAACATCCCTCCCCTGCTCAG
Seq C2 exon
GGCGGCCCTACACACTGAGCGTAGCCCTGCCGGGCTCCATCCTGGACAATGCTCAGTCGCCGGAGCTTCGCACCTACTTGGCCGGTCAGATTGCCAGAGCCTGTGCCATCTTCTGTGTGGATGAGATCGTGGTGTTTGATGAGGAGGGCCAGGATGCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198917-C9orf114:NM_016390:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.674 A=NA C2=0.037
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0259812=Methyltrn_RNA_3=PU(16.8=90.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAAGGATCTCAAGCTGATGA
R:
CATCCTGGCCCTCCTCATCAA
Band lengths:
262-1805
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)