RnoINT0132052 @ rn6
Intron Retention
Gene
ENSRNOG00000018876 | Sdccag3
Description
serologically defined colon cancer antigen 3 [Source:RGD Symbol;Acc:1305930]
Coordinates
chr3:3833819-3834186:-
Coord C1 exon
chr3:3834052-3834186
Coord A exon
chr3:3833969-3834051
Coord C2 exon
chr3:3833819-3833968
Length
83 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGC
5' ss Score
9.44
3' ss Seq
GCTCTCGTTGTCACTTACAGCTC
3' ss Score
9.17
Exon sequences
Seq C1 exon
GGATGAGGCAGGGGCTGGCGACGGCGTTGTGGGCCATGGGGCCGCGGCCGGGTTAGGGCGCGGCGATGTCGGGCTACGCGCGGCGGCAGGGCGCGCCCCCACTATCGCGGACGCGGAGCCTCGTAGTTCCCGACG
Seq A exon
GTGAGCGGCGCGCGGCCGGGGCAGGGCCGGGGGGCGCGGGCGGCGGCGGCCCGCGGTGAAGCCGCTCTCGTTGTCACTTACAG
Seq C2 exon
CTCCTGCGTTCTATGAGCGCCGGTCTTGTCTCCCCCAGCTAGACTGTGAACGCCCCCATGGCGGGGACCTGCACCCCCAGTTCTTCGGCTTTCGGCCGACGTTTATGTGCTATGTGCCCAGCCCGGTGCTGGCTTCGGTAGGAGACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018876:ENSRNOT00000061669:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.667 A=NA C2=0.039
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
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:
GGAGCCTCGTAGTTCCCGAC
R:
TGTGTCTCCTACCGAAGCCAG
Band lengths:
170-253
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]