HsaINT0146373 @ hg19
Intron Retention
Gene
ENSG00000165689 | SDCCAG3
Description
serologically defined colon cancer antigen 3 [Source:HGNC Symbol;Acc:10667]
Coordinates
chr9:139298507-139299145:-
Coord C1 exon
chr9:139299083-139299145
Coord A exon
chr9:139298647-139299082
Coord C2 exon
chr9:139298507-139298646
Length
436 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATT
5' ss Score
8.55
3' ss Seq
AGCCGTAACCGTCCCCCCAGGCG
3' ss Score
6.92
Exon sequences
Seq C1 exon
AAACGGGCTGTAAAGGCAGAAAACCACGTCGTGAAACTAAAACAGGAAATCAGTTTGCTCCAG
Seq A exon
GTAATTAAAGGAAGGGACTTCAGTGTTTTTCTTTGATTTGTGGAGTCACATAATGAATTCAGTAAGAAAGAGGCGAAAGACTCTGCTGGGGTTTCCCCTGAGCCCAAGCAGAGAAAGGACTTCAAATGAGGACAGCAGCCGCTTCCTGTCAGGGCGTGAAGCAGAGGGAGGCCCTGGAGCTCTGTTGGGAGTTTGGGGTCTGGCACGGGGCATCCACTTGTAGGAGTCCCTATTGCCATAGAGCTAGGTGCTGAGCATATACTGGAGTGAAGGGGAAGCCATTAGGCCCCCAGTCCCAGAGGCGAGCCCCCAGTTAGGCCAGAGCATGCATCTTGAGTGCCAGGCCCCCACGGGTAAGCCCTCGCCTCGCCAGGTGGTGACTTTCAGCCGGGTTGCCTCGGAGCTGCTCTGTCCTTAGCCGTAACCGTCCCCCCAG
Seq C2 exon
GCGCAGGTCTCCAACTTCCAGCGAGAGAATGAAGCCCTGCGGTGCGGCCAGGGTGCCAGCCTGACCGTGGTGAAGCAGAACGCCGACGTGGCCCTGCAGAACCTCCGGGTGGTCATGAACAGTGCACAGGCTTCCATCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165689-SDCCAG3:NM_001039708:6
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:
PF0076914=ERM=FE(11.2=100),PF131661=AAA_13=FE(11.8=100),PF0026115=Tropomyosin=FE(18.0=100),PF143571=DUF4404=PD(3.0=9.5),PF052669=DUF724=FE(21.1=100)
A:
NA
C2:
PF0076914=ERM=FE(25.7=100),PF131661=AAA_13=FE(27.7=100),PF0026115=Tropomyosin=PD(12.6=29.8),PF052669=DUF724=PD(15.8=31.9)
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:
ACGGGCTGTAAAGGCAGAAAA
R:
TTGATGGAAGCCTGTGCACTG
Band lengths:
201-637
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)