HsaINT1041090 @ hg38
Intron Retention
Gene
ENSG00000165689 | SDCCAG3
Description
serologically defined colon cancer antigen 3 [Source:HGNC Symbol;Acc:HGNC:10667]
Coordinates
chr9:136404055-136404693:-
Coord C1 exon
chr9:136404631-136404693
Coord A exon
chr9:136404195-136404630
Coord C2 exon
chr9:136404055-136404194
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:ENST00000298537:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
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(12.0=100),PF0026115=Tropomyosin=FE(18.0=100)
A:
NA
C2:
PF0076914=ERM=FE(25.7=100),PF131661=AAA_13=FE(27.7=100),PF0026115=Tropomyosin=PD(12.6=29.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
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]
SPECIAL DATASETS
- Autistic and control brains