HsaINT1041086 @ hg38
Intron Retention
Gene
ENSG00000165689 | SDCCAG3
Description
serologically defined colon cancer antigen 3 [Source:HGNC Symbol;Acc:HGNC:10667]
Coordinates
chr9:136407145-136407938:-
Coord C1 exon
chr9:136407826-136407938
Coord A exon
chr9:136407562-136407825
Coord C2 exon
chr9:136407145-136407561
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:ENST00000298537:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.323 A=NA C2=0.724
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0076914=ERM=PU(8.9=11.5),PF131661=AAA_13=PU(9.0=10.8),PF0026115=Tropomyosin=PU(10.8=8.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
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:
CTGAAGACCAAGAACCTCGGC
R:
GGAAAGGTATGTGCTGCAGGG
Band lengths:
297-561
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains