RnoINT0132055 @ rn6
Intron Retention
Gene
ENSRNOG00000018876 | Sdccag3
Description
serologically defined colon cancer antigen 3 [Source:RGD Symbol;Acc:1305930]
Coordinates
chr3:3831784-3832543:-
Coord C1 exon
chr3:3832428-3832543
Coord A exon
chr3:3832192-3832427
Coord C2 exon
chr3:3831784-3832191
Length
236 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAT
5' ss Score
7.87
3' ss Seq
TTTCTCTCCACTGTTTTTAGGAG
3' ss Score
9.41
Exon sequences
Seq C1 exon
GTGACAAACTTGAAGACCTTGAAGAAGCCAATCCATTCTCCTTCAAAGAGTTTTTGAAAACCAAGAACCTCAGCCTGTCAAAAGAAGACACAGCCACCAGTCGAATTTACCCGAAG
Seq A exon
GTACATCTGGGAAGCTGTCAGTGGTTGCCTTAAAGAAAGTCTCTTGTACCTTACAGCTTTGGAAACTGACTCGAGTGTGGGGAGCAAAGCAGGACAGACATGGCTGCTGGTGGAGAGACTGTGGGTGGAGCGGCCGCTTGGCCCCTTTGGTAGAAGAAATGGGCCCTCTTTGTGGGAGCATAGAGAAGGCCAAGCATTGGCTTCCAGTCCGCAGTGTTTCTCTCCACTGTTTTTAG
Seq C2 exon
GAGGCCTCGAGGCACCCACTGGGACTAGACCACAACTCCCCTGTCTCCCAGCCCATGGGATATGGCCTGGAATATCAGCAGCCATTTTTTGAAGACCCAACAAGAGCCAGCAACCTAGAGGAGGATGAAGAGGACGGGTGGAGCAGAGCCTACCTGCCGTCTGCCGTGGAGCAGACTCACTCCACGAGAGCCACGCAGAACTCATCGCCCTGTGGCACCTACCTTTCCTTCTTTTCCAACGCGTCAGAGCTGGCAGGTCCTGAGTCTTTGCCCCCATGGACACTGAGTGACACTGACTCCAGGCTCTCCCCAGCGTCTCCAGCTGGGAATCCTAATGTAGACTTTGCAGCTCATGAAGAATCCTTAGGGGACAGACACCTGCGGACGCTGCAGTTAAGTTACGAAGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018876:ENSRNOT00000061669:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.359 A=NA C2=0.750
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF057016=WEMBL=PU(12.9=17.6),PF0076914=ERM=PU(10.6=14.0),PF131661=AAA_13=PU(11.5=13.2),PF0026115=Tropomyosin=PU(13.8=12.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
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:
GACACAGCCACCAGTCGAATT
R:
CAAAGACTCAGGACCTGCCAG
Band lengths:
300-536
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]