HsaINT0146375 @ hg19
Intron Retention
Gene
ENSG00000165689 | SDCCAG3
Description
serologically defined colon cancer antigen 3 [Source:HGNC Symbol;Acc:10667]
Coordinates
chr9:139304542-139305054:-
Coord C1 exon
chr9:139304780-139305054
Coord A exon
chr9:139304692-139304779
Coord C2 exon
chr9:139304542-139304691
Length
88 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGC
5' ss Score
9.44
3' ss Seq
GCTGTTGTCGTTGCTTCCAGCTC
3' ss Score
8.14
Exon sequences
Seq C1 exon
GACGGCCCAAGGCGTTCAGGCACGCGCTTTCGGTGCTCGGAGCGGAAGCAGCGGCGAGAGGCTCGGAGGCGCGGGGGCGGCCGAGCGGCGGGCGACGGGGGCGGGCGACGGGGGCGGGCGACGCGGGCCGCGGCACGGGCGGAGCCGGGGCCATGGAGCCGCCGCTGCCGGGCTAGGCAGGTCGTGCCCCGCCGGGCCGGCGGCGATGTCGGGCTACCAGCGCCGCCCGGGCGCCACCCCGCTGTCCCGAGCCCGGAGCCTCGCCATTCCCGACG
Seq A exon
GTGAGCGGGGCAGGGGCCGAGTCCAGCGGTCCAGGTGGGCGGCGGCCGCCCCGGCACGCAGTAAAGTCGCTGTTGTCGTTGCTTCCAG
Seq C2 exon
CTCCAGCGTTCTATGAGCGCCGGTCTTGTCTCCCCCAGCTAAATTGTGAGCGCCCCCATGGCAGGGACCTGGACTCCCCCTTCTTCGGCATTCGGCCGGCCTTTATGTGCTATGTGCCCAGCCCGGTGCTGGCTTCCGTGGGAGACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165689-SDCCAG3:NM_006643:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.750 A=NA C2=0.065
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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:
CGGGCTAGGCAGGTCGTG
R:
CATGGGGGCGCTCACAATTTA
Band lengths:
167-255
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)