HsaINT0146374 @ hg19
Intron Retention
Gene
ENSG00000165689 | SDCCAG3
Description
serologically defined colon cancer antigen 3 [Source:HGNC Symbol;Acc:10667]
Coordinates
chr9:139296374-139298646:-
Coord C1 exon
chr9:139298507-139298646
Coord A exon
chr9:139297340-139298506
Coord C2 exon
chr9:139296374-139297339
Length
1167 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGT
5' ss Score
9.1
3' ss Seq
ATATCCATGCTTGTTTTCAGGCA
3' ss Score
7.23
Exon sequences
Seq C1 exon
GCGCAGGTCTCCAACTTCCAGCGAGAGAATGAAGCCCTGCGGTGCGGCCAGGGTGCCAGCCTGACCGTGGTGAAGCAGAACGCCGACGTGGCCCTGCAGAACCTCCGGGTGGTCATGAACAGTGCACAGGCTTCCATCAA
Seq A exon
GTGAGTGCCTGGGAGGCACCGGGAAGCCTGGCGGGGAAAGGGGTGAGATTGGAGTGGTCGTCAGTGATCCTGGGTGGGGGCCCAGGCTGATGGCACCGTGGCTGGAGGACCAGGGAGCTGCAGGGAGGGACGCGTGCTCAGTGGTCCTGTTAGCTCTCTGGGTCACTGTGTGGACAGACCACAGGCTTTCTAACCTGCCTCGCAGTGTCTGATCCCACCTGGGAGGTGCAGACAGCCACAGCACCCTGCACTGAACCTCAGCCCCACCCCATGTGGGCGCTGAAGCTCTGAATAAAGGAAATAGTGGGGGTTTCCCTCCTGCTGAAAAAGCCACTTCCCAGAAGGCCCTTACTGCTGTGCCTGGCTGGGGACACGCCAGCCACCATGACTGTGACAGTGGTGAGTGTCTGCCACCCATTGGGCTGAGCTCTGCAGGGCGGTGTTGGCCCCCAGAGCACTCCCTGTGAACAAGGGAGCCGTCTCCTGTGAAGTCAGGTGTGGGTCTCCTCCAAGAGGAGCTAGGAGTGGAAAACCTGTGGTTCTCCCCCAGCCCCTCCCTTTCTCCCAGGAACCCTGTCCCTTTCTTCCCCCGGCAAACCCCACCCCTTGCTCCCAGGAACCCTGTCCCTTTCTTCCCCGGCAAACCCCACCCCTTGCTCCCTGGGACCCTGTCCCTTTCTCCCCCGGCAAACCCCACCCCTTGCTCCCTGGAACCCTGTCCCTTTCTCCCCCCGGCAAACCCCACCCCTTGCTCCCTGGGACCCCTTCTGTTTCTCCCCCCAGAATTCTGTCCCTTTCTCCCTGGAACCCCTTACCTTTCTCCCCGCCAGAACCCTTCCCCTGTGGAATCCCTCCCCGCTCTGGAAACCCTCCCCTTCCTTCCCCACCCCCACCCCCGGAATTCCTCCCCTTTCTCCCCCTCAGAACCTCTCCCCTTTTTCTGCCTACCAACCCCTCCCCTTTCTGCCCCCCACCCCCTGTGGAAACCCTCCCCATTCTTCCCCCTGGAAACCCTCGCCTTCCTCCCACTCAGAACCTCTCCCCTTTCCCTACCCCTTGGAACCCCTCCCTTTTTCCCCCTACCAACCCCTCCCCTTTCTCCCCCCAGAACCCTGTTGCTGCTGAGTAGCTGCTGCCACCCATCCTGATATCCATGCTTGTTTTCAG
Seq C2 exon
GCAACTGGTTTCCGGAGCTGAGACACTGAATCTTGTTGCCGAAATCCTTAAATCTATAGACAGAATTTCTGAAGTTAAAGACGAGGAGGAAGACTCTTGAGGACCCCTGGGTGTTCTCAGCATGAAGCTCCGTGTATACCCTGAGGTCACCACCGCTCGATCTAAATGTGCAGTTGTGTCCTTAAATATGCAGTCTTCACCCAGAGTAAAGTGTTGATCGCAAGAGTCCAGTGTCGTGCCCTCAGCCAGTTCTTGGCCACCACAATGGGAGCAGCCCTGGCCGAGTTGTCTCTGTGGTTTCTATGCAGCCCTTCTTGGCGAAATTCCTGCGATCTTATAGATTCTAATGAGCTCTTGGAAGACATTGTCATAAAAGCCAGTGATTTTAAGAAAAAGAGTGGTTCTGGAATCAATGTTTTCCAGTCCCATCCCAGAACATCAGTTGTAAGATAAGTACAATTGGTTGTCCTTGATTTCATAAGTAGAACAAACACTAAATGTGCCTCTGAGATGGCCACCCCGGGCAGGGACCTGTGCCTTCCGCCGATGCTCAGGGCTCCCTCTGGCTCCCGGGTCACTCTTGTGGCCCCAGTGGGTGGTCCCTGCAGTCATGGCCTGAGTGCGCAGGGGCCACCGCGTGGCTGCTGCTGTCCTCCTCCGGGACCCACGGGGACCAAGGTCACACGTTCCGTGCTGTGAAGCTGTCCAGATGTGCCTCTTTGGCTGGGGGTTCTGGTGGACGTTTCAAGTGGCATTTTGTACAATGCAGGTTAGAATTCAGGAATTTCAAGTATGTGCCCGGGTCTGTCAGGTCCCAGTTGCCTTTCTGACGGCCCCCCTCAGAGGGACGGCGATGAGCACTAAATGCTTTTTTGACTATTTTCCTATAGATTTTTTTTAAAACTTTTTTTTCCTCCTGTTCCAATTGATAGCTTTCTTATTTAATAAATTCTGTAGTTCACCGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165689-SDCCAG3:NM_001039708:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.182
Domain overlap (PFAM):
C1:
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)
A:
NA
C2:
PF0076914=ERM=PD(17.9=94.1),PF131661=AAA_13=PD(12.0=58.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCGAGAGAATGAAGCCCTG
R:
CGACACTGGACTCTTGCGATC
Band lengths:
358-1525
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
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)