HsaINT1041087 @ hg38
Intron Retention
Gene
ENSG00000165689 | SDCCAG3
Description
serologically defined colon cancer antigen 3 [Source:HGNC Symbol;Acc:HGNC:10667]
Coordinates
chr9:136405905-136407561:-
Coord C1 exon
chr9:136407145-136407561
Coord A exon
chr9:136405979-136407144
Coord C2 exon
chr9:136405905-136405978
Length
1166 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGT
5' ss Score
9.07
3' ss Seq
AGGATGTTCTCTCTCCACAGCTG
3' ss Score
9.96
Exon sequences
Seq C1 exon
GAAGCCTCGAGGCATTCCCTGGGACTTGACCACAACTCCCCACCCTCCCAAACCGGCGGGTATGGCCTGGAGTATCAGCAGCCATTTTTCGAGGATCCGACAGGGGCTGGTGACCTCCTGGATGAGGAGGAGGATGAGGACACCGGATGGAGTGGGGCCTACCTGCCGTCCGCCATCGAGCAGACTCACCCCGAGAGGGTCCCTGCCGGCACGTCGCCCTGCAGCACATACCTTTCCTTTTTCTCCACCCCGTCGGAGCTGGCAGGGCCTGAGTCTCTGCCCTCGTGGGCGTTGAGTGACACTGATTCTCGCGTGTCTCCGGCCTCTCCGGCAGGGAGTCCTAGCGCAGACTTTGCGGTTCATGGAGAGTCTCTGGGAGACAGGCACCTGCGGACGCTGCAGATAAGTTACGACGCA
Seq A exon
GTAAGTGAGCCTCACGGCGCCCTCTGGCACAGCGCCTGTCCGAGCGGCTTCTCCCGGGGAGAACCTGGAGCCATCCTACCTCTTGGGTGGCCTGGTTTGATTTCCAGGACAAGGCGATTTGCGTGACAGCCTGCTATCCACTTTCCCTTTGACTTTGCTTCTGGTTACACGTGGGAATAGAACCGGCTAAAGAGGACTGGTGAGCTAGAAGCTGTGAATTGGATGCAGTTGGGCACTTACAGGGCTGTACCCTCAGTAAAGGCAGGCTGCAGTCGCCAGCTTGCTAAGTATTCCAAGAGGAGGAAAATTTTTAAAAAATTATAATCACCTAAAAGGTTATAAGCTCTGAATAAAAAAAAAAATTTTTTAGCTGGGCGCCGTGGCTCACGCCTGTAATCTCAGCACTTTGGGAGGCCGAGGTGGGTGGATCACCTGAGGTCAGCAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCTGTCTCTACTGAAAATACAAAAATTAGCTGGGCGTGGCGGCAGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCGGTGAGCCGAGGTCACGCCACTGTACTCCAGCCTAGGCGACGGGCGAAACTCTGTTTCAAAAAAAAGAAAAATTATTTTCTTCCTGAGACAGTGTCTCACTCTGTTGCTCATGCTGGAGTGGAGTGGCACGATCTCGGCTCACTGCAACCTCCGCCTCCCGAGTTCAAGTGATTCTCCTGCTTCAGCCACCCGAGTAGTTAGGACTACAGGTGCCCGCCACCACTGCTGGCTAATTTTTGTATTTTTAGTAGAGACGGGGGTTTCACCGTGTTGGCCAGGCTGGTCTCAAACTCCTGACCTTGTGATCCGCCCACCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGCGAGCCACTGCCCCCGGCCTCTGAGTAAAATTAACTGGCATCTGTGACCACAGGTCTTTGAAAAGTGCCTGCCTCCGTCTGTGGTCTCCCTCTGTAGTGGCTGCAGGTGGATGCTGCACTGACCCAGCATCTCTGCTTATCAGGAGGCTCTGGAGCCACACCGCAGAAGCACACGCCCTTTTGAGCCAGACATGCTGACTTTCTAATAAGGATGTTCTCTCTCCACAG
Seq C2 exon
CTGAAAGATGAAAATTCTAAGCTGAGAAGAAAGCTGAATGAGGTTCAGAGCTTCTCTGAAGCTCAAACAGAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165689:ENST00000298537:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.724 A=NA C2=0.178
Domain overlap (PFAM):
C1:
PF0076914=ERM=PU(8.9=11.5),PF131661=AAA_13=PU(9.0=10.8),PF0026115=Tropomyosin=PU(10.8=8.6)
A:
NA
C2:
PF0076914=ERM=FE(13.4=100),PF131661=AAA_13=FE(14.5=100),PF0026115=Tropomyosin=FE(21.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGAGGAGGATGAGGACACC
R:
AGAGAAGCTCTGAACCTCATTCA
Band lengths:
351-1517
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains