HsaINT0025308 @ hg19
Intron Retention
Gene
ENSG00000198917 | C9orf114
Description
chromosome 9 open reading frame 114 [Source:HGNC Symbol;Acc:26933]
Coordinates
chr9:131584345-131586173:-
Coord C1 exon
chr9:131586026-131586173
Coord A exon
chr9:131585113-131586025
Coord C2 exon
chr9:131584345-131585112
Length
913 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CTGCCACGCTTCTCTTCCAGGAA
3' ss Score
11.31
Exon sequences
Seq C1 exon
GCATGCTCTTGTGGTGTTCGGGGGCCTCCAGGGTCTGGAAGCTGGAGCGGATGCTGACCCCAACCTGGAGGTGGCTGAACCCAGTGTCCTCTTTGACCTGTACGTCAATACCTGTCCTGGCCAGGGTAGCCGTACCATCCGCACGGAG
Seq A exon
GTGAGCCCGCCTGCCTCCCCGACTGCCAGCCACTGGGGCCTTGGGATCTGTCCGAGGGGCGGGTGCTACTCTTGCCCTGTCACCCACCCTTGCCCGTGGCTGCCTTGTCTGGAGGTGGTCCTCTCATCCCCCTTGGCCTCTTGCCACAGCGACGAGACATGAGTGTAGCTGGGAGTCAACCATGGGTGCTAGTGCCCGTCCTGTGCTCCCAGACTGGGTGACCCAGGGGGCCCTGCCCACCCCTGCTCCGGGCCTCTGGTTCCTTAGCCGTGCGCTCAGTGATCTCCCAGGGCCCTGGTTCTGCCACTTCCTTGTGTGTGACCACGGTGGGCACAGCAGCTCTCCCCTTGGGGTCTCACTTGCATCTGTCCCACGGGGGAAGCCACGTGCAGCTGGAGCCTTCGTCCTGGCCTCATGGAACCTGTGTACCCACTTTTGGGGTCAGGCATAGGACGCTGTGCTACGGGAACTCTGCTGGGAAGGCTGGTACTCCCATCAGTCTCGCCGGGCCGACAGCCCTGTCTACCCATCCCTAAGGCCTTGCCCAAGCCGAGCACTCTGAGCCTGACAGCCATACCCCCCAGCAGGAACCCTGGCTGCCACCCTTCCAACCCCTGCACGAGGGGTGAAAACTTCTTGCCCCTCTTCTTGCCCTCCCCTGGCCCTGGGAGGTGGGCGTTGTTACCTTCGCCCCCATTTTACAGAAGAGGAGCCTGAGGAGCAGGCTGTGTGGTCCTCCAGGTGGCAAGTGTGCAGTGTGAACCTGGGCCTGTCATTAACCTCACCAGGCCCTACTAAGGACAGGGGACCCCAGTGGGCCAGGTCTCGGGCAGCCAGGCACTGAAGACAGGCTGGGAGCGGGGGCACCCGCTAGCCCCCCAGGCCCCAGCCCACTGCCACGCTTCTCTTCCAG
Seq C2 exon
GAAGCCATCCTCATCTCCCTGGCCGCCCTGCAGCCTGGCCTCATCCAGGCGGGTGCCCGGCACACCTGAAAGTTCTAAGGGGCCGAGGACATCAGTGAAGCAGCAGTGAAACCAGGGGCTCTGCAGGTCACTTGGGACGGACGCCACCAGACTTGTCTCCAAAAATCACCACCTTTAATACTCCCCGGCCTGCACACACCCACAGTCTCACTGGGCTCCACCCTCACTTACTGCCCGCCGTGATGGCCTTGAGGCTGCCTGCCCGCGCCAGGATGTTTGGCACAAAGAGCAGCCCCGAAGCCCGCTCAATGCTCTCGATGGGCACCAGGAAGCGCTCCAGTGGGATGGCCTCATCCACAGGTGCGTTGGGCATCACGTAGGTGCGGAGCTCAATTTGCCCACCTGCTGCCTCCAGGATCAGCACCTTGAAGAAGTGTGTGGGCACTGCCACGTGGTTCTTGCCGATGACCTGGTACTTTACGTAGGATTTCCCATCAGCCTCTGTCCTGTGGGCAGACCCAGGCACACGTGGGCAGGGGGCCTGGATGAACCCAAAGCCACCTCTTCCAGGCAGCCTTCCCTGATCTGTCCTCTAACTTCTGTCAACCTGCAGGACCACGCCCTCACTGTGAGACTTCTGTAGCCTGCCTGGCTCCTCCTTGAGGCTGGAACTCTCTCCAGGGTGGTTAACTCTTTCCCTCTGTTTTCCTTATGCCCAACACTGGGTCAGGCAGAGTGGGCGACAATAAACGCTGCTAGGAGAATCGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198917-C9orf114:NM_016390:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.500
Domain overlap (PFAM):
C1:
PF0259812=Methyltrn_RNA_3=FE(16.8=100)
A:
NA
C2:
PF0259812=Methyltrn_RNA_3=PD(24.6=45.9)
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:
GCATGCTCTTGTGGTGTTCGG
R:
TGCAGGCCGGGGAGTATTAAA
Band lengths:
342-1255
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)