HsaINT0025659 @ hg19
Intron Retention
Gene
ENSG00000198870 | C9orf96
Description
chromosome 9 open reading frame 96 [Source:HGNC Symbol;Acc:28669]
Coordinates
chr9:136269913-136271220:+
Coord C1 exon
chr9:136269913-136270053
Coord A exon
chr9:136270054-136270375
Coord C2 exon
chr9:136270376-136271220
Length
322 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGA
5' ss Score
7.23
3' ss Seq
CCTTCCTGCTCCACCTGCAGAGG
3' ss Score
10.23
Exon sequences
Seq C1 exon
AGCTGGCGGCCTTCAAGGTGGTGGTGCAGGAGGAGGGCGGCAGTGGCCTCAGCCTCATCAAGGAGACCTACCAGCTCCACAGGGACGACCCGGAGGTGGTGGAGAACGTGGGCATGCTGCTGGTCCACCTGGCTTCCTATG
Seq A exon
GTGAGAACCCCTTCTCACCTCACACTCCCTAGAGCCCAGCGGTCAGGGGTGCCCCGCTCCCCCTATAACTGACAGGGAAGGAGCACATGGAAGGTGGGCTCAACCCCACTTCTCGGCCCACTTAAACTTCCCACTCATTTGGCATCTTCTGAGCACCAGGGGTTGTCCTGGCTGAGGGTGACGCTTGGGGCTCCGGAACTGCAAGGTGGCTCTGTGCATGCCAAGCCCAAGGGGGAATGTGACCCACTCTCATCCTTCTGGGGCTTCTGGCAAGGGGCACAGGAAGGACTCTGGCCTCAGGACCTTCCTGCTCCACCTGCAG
Seq C2 exon
AGGAGATCCTGCCGGAGCTGGTGTCCAGTAGTATGAAGGCCCTGCTCCAGGAGATCAAGGAGCGCTTCACCTCCAGCCTGGTGAGTGACAGCAGCGCCTTCAGCAAACCAGGCCTCCCTCCAGGTGGAAGCCCCCAGCTGGGGTGCACCACGTCTGGGGGACTGGAATAGATGTTTGTATGGAACTGACCTTGATCTCCACGTGTATAGTTTTCAAGACTGCTCTCCTGCCTGCCTATTATCCCATCTCTATGACTGGGCCAAAATCAATCTTAAACGGGAGGGGTAATCAGACCTCTCCAAAGAGTTTCCTGTCCATGACTGCTGGATTGAGTCACATGAGTAACTGCTCCTGGACCCGGGGACTGTCCACGAAAACTGACTTGCCTGCTTCCTCCTTCCAGGAACTGGTTTCTTGCGCGGAAAAAGTGCTCTTGAGGCTGGAGGCAGCCACCTCTCCCAGCCCACTGGGTGGGGAAGCAGCTCAGCCCTGATGCGGGGGAGAAGACAGATACCCCACAGGCCCCTCCCTCCACGTGTGCCCTCTCCCTGTCCTTCCTTTCCATGGGCCACTGTTTCCCTTGGGGTGGGGGGAAGGGTCATCCAGCACCAGAATGCGCACCTCACACTCCTCTTAGGTGACTAATAAAGAGGCCCAAGGCCAGTTTCTGCCTTAATCATTTCTGGCAAGAGGCTGTGACTGGCCAGTGGGATACTTAATTCTGCAGTCTCTATAGACCTCGCCCCTGGACAGAGCAGTCCTTCCAGACCATTCTAGATGAGAGTCAACACTGAGCCTCCACAGGCTCCATTCCAAGTAAACATCTGCATTTATTTTAAATCGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198870-C9orf96:NM_153710:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.375
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGGAGACCTACCAGCTCCAC
R:
TGGCCCAGTCATAGAGATGGG
Band lengths:
344-666
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)