HsaINT0025323 @ hg19
Intron Retention
Gene
ENSG00000160401 | C9orf117
Description
chromosome 9 open reading frame 117 [Source:HGNC Symbol;Acc:27843]
Coordinates
chr9:130474099-130474628:+
Coord C1 exon
chr9:130474099-130474229
Coord A exon
chr9:130474230-130474477
Coord C2 exon
chr9:130474478-130474628
Length
248 bp
Sequences
Splice sites
5' ss Seq
GAAGTGCGT
5' ss Score
4.88
3' ss Seq
TCATCCCAGTTGGGGTCCAGGAG
3' ss Score
-0.56
Exon sequences
Seq C1 exon
ATCATCCTCATGCTGACTAAGAAGTGCCAGGAGCAGCAGCAGGACACCAAGGAGGCCGAGGAGCTGCGCCTCCTGCTGAGCCAGTTGGAGCAGAGATCCCTGCAGCTGCAGGTGGATAACCAGGCACTGAA
Seq A exon
GTGCGTATGGCCCACGGAGGGGCGGGCGGCGGGTGCAGGCTGGGGCCAAGCTCTGGCCCAGCTCTTTCCGATCCCACGACCCAGGCCAGTGACTTCCCCTCTCTAGAGGAGCCTGCCAGACAGGCTGAGGCTTGGGGCGGGATGGGGGCCCCTGTGGGCTTGGAGAGAAATGGCAGGGCCCCTGGCCCCAGGTGGCCCCAGTCCTGGGGAAGGGGGAAGGCTGTTGACTCATCCCAGTTGGGGTCCAG
Seq C2 exon
GAGCCAGAGAGACCAGCTGAGCCTGCAGCTGGAGCAGCAGCAGGTGGATTTGCAGCGGCTACAGCAGGAACTGGCTAATGAGCAGAAGGTTCGGGCCAGCCTGGAGGCGGCTCTGGTCCAGGCCACCTCCTTCCTACAGAACATTCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000160401-C9orf117:NM_001012502:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.023 A=NA C2=0.039
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
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:
TCATCCTCATGCTGACTAAGAAGTG
R:
GAATGTTCTGTAGGAAGGAGGTGG
Band lengths:
276-524
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)