HsaINT0025655 @ hg19
Intron Retention
Gene
ENSG00000198870 | C9orf96
Description
chromosome 9 open reading frame 96 [Source:HGNC Symbol;Acc:28669]
Coordinates
chr9:136266867-136268141:+
Coord C1 exon
chr9:136266867-136267007
Coord A exon
chr9:136267008-136268006
Coord C2 exon
chr9:136268007-136268141
Length
999 bp
Sequences
Splice sites
5' ss Seq
AGGGTGTGT
5' ss Score
4.51
3' ss Seq
TCATTCTGGCTCACCCACAGAGT
3' ss Score
7.75
Exon sequences
Seq C1 exon
CGCTGGTGCACCACCCGGAAGCCAAGGCTCCCTGCAACCAAGCCATCACCTCCACCCTGCTGAGTGCTCTTCAGAGCCACCCCGAGGAGGAGCCACTTCTTGTCATGGTCTACAGCCTGCTAGCCATCACCACAACCCAGG
Seq A exon
GTGTGTCTGCCAGCCACCTCCTGCCCCACCCACGCTCCAGGACAGCCCTTCCCAGGGGTCTTGGAAGGGTTGGTTTGGGGTATAGGTGGGTTGGACAGGACAGTGCTGGGCCTCCTCCTGAGATACATGGTGGCATTTGGCCGTCTTCATTTGGCCACCCCAAATGCTGGTCGCATCCTTTTCCATCTTGATGACAAGCTTCCACTCTTGAAGTCACTGGTTCCCTCTACAGACATGCTAGGCGCAGCTGTGGGCTTCACACCAATGACATCTCTTTCCCACACTTCCTGCCCCTTCTGGGAGGCTGGGGCTCAAATGCCCTGTGTGTCTCCATTCCATAGGGCCCAGTGGGCTTCCGAAGCCGCCAGCCAGGACTGTGGGAAGGAGAGGGCCATACAGAGCGCTCACACCTTCACCCACAAATCGGGTGGGCACTGTTCTCCCCAACAGGAAGCTGGGCCTCGAGAGAGCCTAAGGACAGTTGCCAGGAGTCCATGCAGCAGGGTTCAGGGCTGGGGTCTGGGCCCCAGCACCCTCTTTACTGCACAGACTGGATAACTGATGATACATGGCTGATCTCACTTTGGGGAGTGAAAGGAGGCACTAGGAATAGATGTCAACTGGAACCCTCAGGCAAAATGGATGTCAGTTCATCCTACCGGGATAGGGCCCCGTCATGGTTCCATCCTGGAAGGCACAGGCTGGCTCTGTGAGCCCAGGAGGCAGGGTCAGGCCCCCTGGATGGGAAGCTACAGAGGTCAGACCCAGCCTGGTAGTGGGATGGCAGCTATTGGGACTGGTGGTCCACGAGATGGACAGACTCCTCTGGGGCCAGTCCCACATCCTCCTGTTCAGGGCTCCATTGAGTGCACACGACTTGGCCCAGAGCAGGCACCTAGGATTGCAGGTCAAATGGGACTGCAGTGCCCAAGGACAACAGAGGCAGGAAGGCTTCCTGGAGGGAGGGGCCCTGGGGCCCTCATTCTGGCTCACCCACAG
Seq C2 exon
AGTCAGAGTCACTGTCAGAGGAGCTGCAGAACGCTGGGCTGCTGGAGCACATCCTGGAGCACCTCAACAGCTCCCTCAAAAGCAGGGACGTCTGCGCCAGCGGCCTGGGCCTGCTCTGGGCCCTCCTGCTGGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198870-C9orf96:NM_153710:13
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:
PF050048=IFRD=FE(39.2=100)
A:
NA
C2:
PF050048=IFRD=FE(37.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
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:
CACCACCCGGAAGCCAAG
R:
CAGCAGGAGGGCCCAGAG
Band lengths:
264-1263
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)