HsaINT0025326 @ hg19
Intron Retention
Gene
ENSG00000160401 | C9orf117
Description
chromosome 9 open reading frame 117 [Source:HGNC Symbol;Acc:27843]
Coordinates
chr9:130475299-130476303:+
Coord C1 exon
chr9:130475299-130475485
Coord A exon
chr9:130475486-130476112
Coord C2 exon
chr9:130476113-130476303
Length
627 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
CAGCATCTTTAATCTTACAGATG
3' ss Score
7.53
Exon sequences
Seq C1 exon
CCGGCCCAGCATCCAGCTGCCCAGGACTGGGTCTCTGCTGCCGCAGCTCTCTGACATCACCCCCTACCAGCCGGGGGATCTAGGCCTGGTACCTCGCCAGGTCCACATCCCACCCAACCCCCAGGACCTCAGGCTGCTGTCATATATCACCCGTGTGGGGACCTTCCGGGCACACAGCAGCCCTGAG
Seq A exon
GTGAGGGTGCCAGGGGCCCCAGGGAAAGCAAGGTGGCAGCTAGTCCTGGGTACAAACTGAGGCTCTGCCAGGCCACAGCTGTGTGGCCCTGGGGATGTAACCAGATCTCTCTGAGCCTTCCCATCTGTAAAATGGGCTGAAGAAAGGAGTGGCCAAGCCTCAATGGGCCAAAGCATGCCCACACATGCCCTGGGAGGGGGGTTGGCTGGACCCTGTTCTTCCCTCCCCCACCAGCAGGGAAAGAGTGGGATCCCCCTGAAGAGGCCTCAGCTTCCAAGCCAGCATCTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTCACTCTGTCACCCAGACTGGAGTGCAGTGCCACAATCTCAGCTCACAGCAACCTCCGCCTCCCAGGTTCAAGTGATTCTCCTGCCTCAGTCTCCCAAGTAGCAGGGATTACAGGCATGCACCACCATGCCTGGCTACTTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACGTCAAGCAATCCCCCAGCCTCGGCCTCCCAAAGTGCTGGGATTATAGGTGTGAGCCACTGCACCCGGCCTCCAAGCCAGCATCTTTAATCTTACAG
Seq C2 exon
ATGCGTGCCCCTGGTTCTCTAAAAAGGCTTGAAAAGTTTAGTCTTCCTGAAGTTCCCCTACGTCCCAAGTAGGACACAGAGAGAAGAACCTACTCCAGAAATGGACTGGTCCAGTCACAGTCACCCCCACTTTAATCCGCAGGCAGCCTGGAACAGTCTAGAGGAGATTTGTATAAAAAGTAGATACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000160401-C9orf117:NM_001012502:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.571 A=NA C2=0.957
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
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:
ATCCAGCTGCCCAGGACTG
R:
TCTCCTCTAGACTGTTCCAGGC
Band lengths:
344-971
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)