HsaINT0025652 @ hg19
Intron Retention
Gene
ENSG00000198870 | C9orf96
Description
chromosome 9 open reading frame 96 [Source:HGNC Symbol;Acc:28669]
Coordinates
chr9:136262291-136263182:+
Coord C1 exon
chr9:136262291-136262421
Coord A exon
chr9:136262422-136263098
Coord C2 exon
chr9:136263099-136263182
Length
677 bp
Sequences
Splice sites
5' ss Seq
TAGGTGATG
5' ss Score
3.49
3' ss Seq
CTGCCTTCCTGTCCCTGCAGAGG
3' ss Score
12.06
Exon sequences
Seq C1 exon
GGACGTGGTGCACATCACCTTCTTGAGAGGCTCCTTCAAGTCCTCGTGCGTCTCTCTGACCCTGCACCGGCAGATGGTGCCTGCGTCCATCACCGACATGCTGTTAGAAGGCAACGTGGCCAGCATTTTAG
Seq A exon
GTGATGCTGGGGACACAAAGGGGGAGCGTGCCCTGAAGCTCCTGTCCATGGCCTTGGCATCCTATTGTTTAGTTCCAGAGGGTTCATTATTTATGCCCCTGGCCTTGCTCCACATGCACGACCAGTGGGTAGGAACAGTTTCCCTCCATCCATCCCTACACACTGCCCAGGACACCGCTCTGCTCAAATATCCTCCATAGCTCCCAACTACCTATAACACAAAGTTCCTCTCCATAGCCTGGCCCCCACCTGTTTTCCCTCCGCTCCTGCTACACAAATCCTCTATGTAGCTCAATGGCCTAGTCACTGCCCACGCCTCCCACAACCCTCTGCTTTTGCTTCCACAGCCTGGGTGGCACACAGTGGTCCCAGGACATCTTCCTCACACAGCACCACTTCCTTCCTGCGTGCTTCTATGTGCCCAGGATGAGCAGAAGTGCGCTCCATCATCTGTGTGCTCCAAGACAGAGACTTGGGTTCTATTAAGGAAAAGTTGCTTGGTCTCAGTGGCCTCATCTGTAAAGTGGGGATGGTAACAGCCCCTCCCTCTCATCCTGAACCTGTGGATCTGAGGAGGGGATGCACACACAGCAGCCAGCCCAGTGTGGTGCCGAGAAACAGAGCCCCGAGGCCCTGGTCCTCAGAAAGGTCCCTCCCCTGCCTTCCTGTCCCTGCAG
Seq C2 exon
AGGTCATGCAGAAATTCTCTGGCTGGCCCGAAGTCCAGCTCAGGGCCATGAAGAGGCTTCTGAAAATGCCTGCAGATCAGCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198870-C9orf96:NM_153710:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=PD(3.0=17.8)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
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:
GGACGTGGTGCACATCAC
R:
TAGCTGATCTGCAGGCATTTTCA
Band lengths:
214-891
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)