HsaINT0146367 @ hg19
Intron Retention
Gene
ENSG00000165689 | SDCCAG3
Description
serologically defined colon cancer antigen 3 [Source:HGNC Symbol;Acc:10667]
Coordinates
chr9:139302278-139303519:-
Coord C1 exon
chr9:139303451-139303519
Coord A exon
chr9:139302391-139303450
Coord C2 exon
chr9:139302278-139302390
Length
1060 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGAG
5' ss Score
4.86
3' ss Seq
TGTGATGTCTGTTATTTCAGATG
3' ss Score
8.09
Exon sequences
Seq C1 exon
ATTTTGGCTATGGAAAGGGGAAATGTTCTAAGCAGAGCCCGTCAGGAGCCCACGGGACACATTTTGGAG
Seq A exon
GTAGAGTAGTTCAGCAACCTTTTCTTCTTGTCTCCATCCAACACAGTGCCAGGCACGTGTCTGGTGGGACTGTCAATGTGACTGGCTATGTGGTGTAGCTGGAGCCCAAAAGAGCAGGTGGGGGTGGGATTTCAAGGGTTCAGTCTTGATCCTAGAGTAGCAGCGAGGTGACATCAGGGAGCGGGGAAGCCCCACCTGGGGGGCTGGGGCCACAGGAGCCAGCTTTACATGGGGCTCACAGCTGGGAGGGTCGAGTGTGGCTGCTTAAGTCCCCGGAGGGTGGGAAGGCGGTGGCAAGAGGGAGAAGGGAAAAGTGGGCGTTATTTAGGCTACCTAGGTAGGAAAGTCGGGAAGAGGGTCAGGGGGCACTGGGTCCCCAGCGTTGCAGCACCTGAGGAGCTGGTTGTTGTTGTTGTTTTTTGAGACAGAGTCTCGCTCTGTCGCCCAGGCTGGAGTACAGTGGCACGATCTCGGCTCACTGCAAGCTCCACCTCCCAGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCTCACCACCACGCCTGGCTAATTTTTTGTATTTTTAGTAGAGATGAGGTTTCACCGTGTTAGCCAGGATGGTCTCAGTCTCCTGACCTCGTGATCCGCCCGCCTTGACCTCCCACAGTGCTGGGGTACAGGCGTGAGCCACCACACCTGGCCACCTGAGGAGCTTTGAGAGCTCCTAGCACAGGTTGACCTCACACCAGGGAGCTGGGTGTGTGCAGTGGAGTGGCTTGGGTCGTTTTAAAGCTCCCCAGGGGAGCTTTAGTGAGCAGCACAGTGTGGGAGCAGGGGCCGAGGGGTGGAAGGAGAAGATTGCAAATGCAGACGCACGTCTGTGTCACTGCCCACCTTCAGCCACCTTCACACTTCCTAGTGCTGCCTGAGTCATGGTAGAATGACAAGCGTGGCTGCCCGATCTCACATGTGGCCATGCTCTGGAAAGACAGGTGAACAGGAAGGTTCCCTTTCAACGCTCTTCAGTAGACTTTATGCATTTGTGATGTCTGTTATTTCAG
Seq C2 exon
ATGACAGATTTGAAGATCTGGAAGAGGCAAATCCATTCTCTTTTAGAGAGTTTCTGAAGACCAAGAACCTCGGCCTCTCGAAAGAGGATCCGGCCAGCAGAATTTATGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165689-SDCCAG3:NM_001039707:3
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.778 A=NA C2=0.318
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion 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:
ATTTTGGCTATGGAAAGGGGA
R:
CTTTGCATAAATTCTGCTGGCCG
Band lengths:
182-1242
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)