HsaINT0146369 @ hg19
Intron Retention
Gene
ENSG00000165689 | SDCCAG3
Description
serologically defined colon cancer antigen 3 [Source:HGNC Symbol;Acc:10667]
Coordinates
chr9:139301597-139302390:-
Coord C1 exon
chr9:139302278-139302390
Coord A exon
chr9:139302014-139302277
Coord C2 exon
chr9:139301597-139302013
Length
264 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAT
5' ss Score
8.88
3' ss Seq
TTTTTTTTTTTTTTTTTTAGGAA
3' ss Score
13.15
Exon sequences
Seq C1 exon
ATGACAGATTTGAAGATCTGGAAGAGGCAAATCCATTCTCTTTTAGAGAGTTTCTGAAGACCAAGAACCTCGGCCTCTCGAAAGAGGATCCGGCCAGCAGAATTTATGCAAAG
Seq A exon
GTAAATCCACGGCACTGTGGGCGATGGCTCTGTGGGACGTTTCTGTTCCGGCCTCTGCAGCCTCCTTTGGAGGAATCGTGCATGAGTGTGGCAGAGCAGGCAGGCGTCAGTGCTGGGGAGCAGCTCTGGGCTCAGAAGCTGCTGGGCTCCTTCCGGTAGAGAGATTGGGCCTTTCTTCTTGTTGCGAGGCAGAACACAGAAAGGAAGATGCGCTCCGAGTCAGAAGCATGGCCTCCATTGTTTTTTTTTTTTTTTTTTTTTTAG
Seq C2 exon
GAAGCCTCGAGGCATTCCCTGGGACTTGACCACAACTCCCCACCCTCCCAAACCGGCGGGTATGGCCTGGAGTATCAGCAGCCATTTTTCGAGGATCCGACAGGGGCTGGTGACCTCCTGGATGAGGAGGAGGATGAGGACACCGGATGGAGTGGGGCCTACCTGCCGTCCGCCATCGAGCAGACTCACCCCGAGAGGGTCCCTGCCGGCACGTCGCCCTGCAGCACATACCTTTCCTTTTTCTCCACCCCGTCGGAGCTGGCAGGGCCTGAGTCTCTGCCCTCGTGGGCGTTGAGTGACACTGATTCTCGCGTGTCTCCGGCCTCTCCGGCAGGGAGTCCTAGCGCAGACTTTGCGGTTCATGGAGAGTCTCTGGGAGACAGGCACCTGCGGACGCTGCAGATAAGTTACGACGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165689-SDCCAG3:NM_001039708:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.318 A=NA C2=0.727
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0076914=ERM=PU(8.9=11.5),PF131661=AAA_13=PU(8.9=10.8),PF0026115=Tropomyosin=PU(10.8=8.6),PF143571=DUF4404=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGAAGACCAAGAACCTCGGC
R:
GGAAAGGTATGTGCTGCAGGG
Band lengths:
297-561
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)