HsaINT0025320 @ hg19
Intron Retention
Gene
ENSG00000160401 | C9orf117
Description
chromosome 9 open reading frame 117 [Source:HGNC Symbol;Acc:27843]
Coordinates
chr9:130471701-130473033:+
Coord C1 exon
chr9:130471701-130471972
Coord A exon
chr9:130471973-130472879
Coord C2 exon
chr9:130472880-130473033
Length
907 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGG
5' ss Score
6.9
3' ss Seq
TTGTGCGCTGTGGCGGCCAGGGG
3' ss Score
4.03
Exon sequences
Seq C1 exon
GTACCAGCGGAAGTGGGATGAGCTGGCTGTGCAGGAGAAGATGTTCCGCCAGGAGTTTGAGCAGCTGGCCAATAACAAGAAGGAGATTGTGGCCTTCCTCAAGCGCACGCTCAACCAGCAGGTGGATGAGATCACAGACCTCAACGAGCAGCTCCAGAACTTGCAGCTAGCCAAAGAGATGGAGAAGGATGCCTTCGAGGCGCAGCTGGCCCAGGTGCGCCACGAGTTCCAGGAGACCAAGGACCAGCTCACCACGGAGAACATCATCCTTG
Seq A exon
GTGAGGAGGGGACTGGCTGGTGAGCCTGCAGGCACACATCCCAGCTCTATCACTGACCCTGTTTCTCACCTGGGAAACAGGGATAATAGCCACATGCTGCTTGGCACACACTGTCTTCCTTAATTGTCCCAGCAATCCTACGAAGCTGGAAACATCCCCCAACCAGTTTGTAGACAAGGAAGCACCTCAAAAGATGAAGTGTCGTGACCAAGGTCCCCCAGTTGGCAAGGGTTGTGAGGCTCAAATGTCAGATGGCATTAGAACCTAGCCCAGAGAATATATACAGTCCAGCTGCTGGCTGGGCGTGGTGGCCCATGCCTGTAAAACCCTGTGCTTTAGGAGGCCAAGGCGGGAGGATTGCTTGAGCCCAGGAGCTTGAGACAAGCCTAGGCAACATAGCGACACTCCATCTCTACCAAAAAAATACAAAAATTAGCCAGGTGTGGTGGTGCACATATGTAGTCCCAGCTACTTGGGAAGCTGAGGTGGGAGGATCTCTTGAGCCTGGGAGGCTGGGAGGTTGAGACTGCAGTGAGCTGTGACTGTGCCACTGCACTCCAGCCTGAGTGACAGAGGAAGACCCTGTCTCAAAAAAAAAAAAAAAAACAAAACAGTTGTTGTCATTACTGTCGCTTTCATGAGAGTATCAAGGAAGGCTTCTTGGAGGAGGTGGAACCTGAACAAAACTTCATAAGATTCATGGAGGGGTGGAGGGAGGGCAACCCAGATGAAGGCAGTAAAGGTGACAGGGCCAGGCAGGGTAGGTGGGGGATGGTAGACCTGCCCCACTGAGACCACACAGGGCGCACAGGAAGGGACAGGGACCTAAGGGGCATCTTTAAGGTCCTCGCCAGGCCCTGTCCTCTGAGGCAGCCCATCATTGGGCCTTGTGCGCTGTGGCGGCCAG
Seq C2 exon
GGGGGAAGCTGGCAGCCCTGGAGGAGTTCCGGCTGCAGAAAGAGGAGGTCACGGACAAGTTCACATTGCTGGAGGAGCAGGTGCGGAAGCAGGAGAATGAGTTCAGGGACTATGCATACAACCTGGAGAAGAAGTCGGTGCTGGACAAGGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000160401-C9orf117:NM_001012502:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGCTGTGCAGGAGAAGATG
R:
AACTCATTCTCCTGCTTCCGC
Band lengths:
353-1260
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)