HsaINT0025394 @ hg19
Intron Retention
Gene
ENSG00000197768 | C9orf173
Description
chromosome 9 open reading frame 173 [Source:HGNC Symbol;Acc:37285]
Coordinates
chr9:140147114-140147934:+
Coord C1 exon
chr9:140147114-140147417
Coord A exon
chr9:140147418-140147566
Coord C2 exon
chr9:140147567-140147934
Length
149 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGG
5' ss Score
4.84
3' ss Seq
CCAGCCTTCTCTTTCGGCAGCCC
3' ss Score
6.99
Exon sequences
Seq C1 exon
TGGCCCTCGCCAGCCCACTACCAGCTGCTCAGCCGGCCCGCCTTCCCCGCCTTCAGCTTCAGAGGCTGCCACTCCGCTTCCAAGACACCTGAAGGCCACACCCACCTAGGGCTGCCTGGGGCTAGGGGGCTGGGCCTCAGGGTGCAGCCCCAGTCCCTGCTTCAGGCCTCTTTGCAGGCACCTGGCAAGAGATGCCCTGGCCCCAACACCTACAATATCCTTCCTGGGAGCCGCCTGCAGAGCCCCCGCTCGCCGGCCTTCTCGATGAGCCGCTCCCCTGCGTTCACCTCCTGGCTCAGCACCT
Seq A exon
GTAAGGAGGCCTGGAGAGAAGAGGGCTAGGGATGGGGCATGGGTGGGCAATGTGAGGACAAGGGTTCAGGGGCCGGGGGTGGGAACTGGGAGCCAGGTTTGAGTTGGGGCTGCTACCTGGGTGGGGCTCCCAGCCTTCTCTTTCGGCAG
Seq C2 exon
CCCGAACCCCTGGCCCAGCCGCCTACCACGTGGAGGACTGCAACTCACGCTTCCCTTCGGCGCCTGGCGTGGTCATCCAGGGTGTACGCAGACCCAAGCGCCACGACACAGGCCCCTTCTGCACGCTCTAGAGCCAGCTGGGCACAACCTGCTTGGCCCGGCCACCGAGTGGAACCATGGCCTCCCCCGGGGCTTTCCCAGGCCTCCCCTGGGACTTGGGGCCCCAGCCTGGCCTTCTGACCCTCTGGGCACCCCGATGCACCCTTCTGGCTGGCCAACCCTTCTATGGGCTGTGGACAAGGCTGGCCCAGCCTGGATCCCCCATCTGCCCATCTCCCCGCTACACTGAGATGCTGTTGGTTTTCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197768-C9orf173:NM_001004353:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.542 A=NA C2=0.542
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
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:
CCTGCTTCAGGCCTCTTTGC
R:
GTCTGCGTACACCCTGGATGA
Band lengths:
242-391
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)