HsaINT0146368 @ hg38
Intron Retention
Gene
ENSG00000165689 | SDCCAG3
Description
serologically defined colon cancer antigen 3 [Source:HGNC Symbol;Acc:HGNC:10667]
Coordinates
chr9:136410090-136410609:-
Coord C1 exon
chr9:136410328-136410609
Coord A exon
chr9:136410240-136410327
Coord C2 exon
chr9:136410090-136410239
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
CCTCGCCGACGGCCCAAGGCGTTCAGGCACGCGCTTTCGGTGCTCGGAGCGGAAGCAGCGGCGAGAGGCTCGGAGGCGCGGGGGCGGCCGAGCGGCGGGCGACGGGGGCGGGCGACGGGGGCGGGCGACGCGGGCCGCGGCACGGGCGGAGCCGGGGCCATGGAGCCGCCGCTGCCGGGCTAGGCAGGTCGTGCCCCGCCGGGCCGGCGGCGATGTCGGGCTACCAGCGCCGCCCGGGCGCCACCCCGCTGTCCCGAGCCCGGAGCCTCGCCATTCCCGACG
Seq A exon
GTGAGCGGGGCAGGGGCCGAGTCCAGCGGTCCAGGTGGGCGGCGGCCGCCCCGGCACGCAGTAAAGTCGCTGTTGTCGTTGCTTCCAG
Seq C2 exon
CTCCAGCGTTCTATGAGCGCCGGTCTTGTCTCCCCCAGCTAAATTGTGAGCGCCCCCATGGCAGGGACCTGGACTCCCCCTTCTTCGGCATTCGGCCGGCCTTTATGTGCTATGTGCCCAGCCCGGTGCTGGCTTCCGTGGGAGACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165689:ENST00000298537:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.667 A=NA C2=0.069
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
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]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development