HsaINT0025355 @ hg19
Intron Retention
Gene
ENSG00000186193 | C9orf140
Description
suppressor APC domain containing 2 [Source:HGNC Symbol;Acc:28055]
Coordinates
chr9:139959974-139960826:-
Coord C1 exon
chr9:139960714-139960826
Coord A exon
chr9:139960121-139960713
Coord C2 exon
chr9:139959974-139960120
Length
593 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGC
5' ss Score
8.05
3' ss Seq
TGTAAATGCACGTATTGCAGCTG
3' ss Score
5.27
Exon sequences
Seq C1 exon
GTGCAGTGGCGTGCAGGGCCCTGGAGGCGGACTCAGGGGATGCCCGGCGGGCTCCCCGTGCCCGAGGGGAACGTCGGAGGCACACCATCGCCAGCGGCGTGGACTGCGGCCTG
Seq A exon
GTGAGCAGGGACTGGGGCTCTGTGGGGCTCTCCATCTTGCCTGGAGGCTGGAGGCCGGGATGGGAGCAGGGGGGCCTTGAGCCTGGGGGAGTCCATGGCGGAAGTACAGTCAGCTCTGGACATCTCTCTCCCTACCTGGGCTTGACTCCCCTGGAGGGATGGCCCAGGGTCAGGCAGAGGGAGGTCAAGAGGTCGTTTAGGGCAGCTATGGTGGCTGCCCAGCCCGCCTCACGAGGTTGCTGCTGCAAGCCAGTCTGGCTTCCCAGCTGTGTGCTCACCACAGGCAGACTTCGGGAGGGTGGGCTCAGCTGAAGGGTCCGTCACCCCTCCCCCAGGGAAGCCTGAGTGGAGGGGCTAAGAAAGGCCAAGACCCCTCAGCAGGAGGAACGGGGCTCCTGCTCCAAATGGGCCTATGGGGCTCACACATGCAGGTGTCAGCAGAAGCGTGCGTCCGTGGGTGTTTGCAAACGTGTACACGTGCTGCTGCATTTGTGTCTGTGGCTCTGGTGCCCACCCACAGGTGAGCTCATGCATGTGTGGACGTGTGCGTGCTCACTGGGGCCAGGCATTCCATGTAAATGCACGTATTGCAG
Seq C2 exon
CTGAAGCAGATGAAGGAGCTGGAGCAGGAGAAGGAGGTGCTGCTGCAGGGTTTGGAGATGATGGCGCGGGGCCGCGACTGGTACCAGCAGCAGCTGCAACGAGTGCAGGAGCGCCAGCGCCGCCTGGGCCAGAGCAGAGCCAGCGCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000186193-C9orf140:NM_178448:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.667 A=NA C2=0.497
Domain overlap (PFAM):
C1:
PF114143=Suppressor_APC=PU(4.8=10.5)
A:
NA
C2:
PF114143=Suppressor_APC=FE(57.1=100),PF097894=DUF2353=PU(29.1=93.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGCGGACTCAGGGGATG
R:
GCTCTGCTCTGGCCCAGG
Band lengths:
230-823
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)