RnoINT0132057 @ rn6
Intron Retention
Gene
ENSRNOG00000018876 | Sdccag3
Description
serologically defined colon cancer antigen 3 [Source:RGD Symbol;Acc:1305930]
Coordinates
chr3:3830433-3830989:-
Coord C1 exon
chr3:3830916-3830989
Coord A exon
chr3:3830545-3830915
Coord C2 exon
chr3:3830433-3830544
Length
371 bp
Sequences
Splice sites
5' ss Seq
AATGTATGT
5' ss Score
5.87
3' ss Seq
CTCCATTTTTCCTTACTGAGGGT
3' ss Score
-7.52
Exon sequences
Seq C1 exon
CTGAAAGATGAAAACTCTAAGCTCAGAAGAAAGCTAAGTGAGGTTCAGAGCTTCTCTGAAACTCAAACAGAAAT
Seq A exon
GTATGTAAACTTGTAGTTAGGTGTCACCTTAAAAACCACCTCTACCATTCAGGGAACTCGGTTCCAAGGGCTGAGGGGCATAGCTGCTTGTCATCCTTAAATCTAAAGCAGCAAACACATCTTCTTGTTCTGTTTTAGTCTTTTTAAGACACAAATCAGCTGAGTTTTGTCTTGGTTGGCAGACTTGAGAAAATGGTATCTGGGCCTTCCACAGGGAGCATGAAGCTGGGCGGTCATTGCTACCCTGCGGCTGCCTGAGGCAGCTTCTCCATCCATGGCTCTAGTGGGTCTCACCGTTAGTCAGGCTACAGTGCTGTTGGAAGCACTCTTGGCAGGGCCTGGAGAACTCAACTCCATTTTTCCTTACTGAG
Seq C2 exon
GGTGAGGACGCTCGAACGGAAGTTGGAGGCGAAGATGATCAAGGAAGAGAGTGACTTCCATGACCTGGAGTCAGTAGTCCAGCAAGTCGAACAGAACCTCGAACTGATGACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018876:ENSRNOT00000061669:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.440 A=NA C2=0.263
Domain overlap (PFAM):
C1:
PF057016=WEMBL=FE(12.9=100),PF0076914=ERM=FE(13.3=100),PF131661=AAA_13=FE(15.3=100),PF0026115=Tropomyosin=FE(19.5=100)
A:
NA
C2:
PF057016=WEMBL=FE(19.9=100),PF0076914=ERM=FE(20.6=100),PF131661=AAA_13=FE(23.6=100),PF0026115=Tropomyosin=FE(30.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAAAGATGAAAACTCTAAGCTCAGA
R:
GGTCATCAGTTCGAGGTTCTGT
Band lengths:
185-556
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]