RnoINT0132054 @ rn6
Intron Retention
Gene
ENSRNOG00000018876 | Sdccag3
Description
serologically defined colon cancer antigen 3 [Source:RGD Symbol;Acc:1305930]
Coordinates
chr3:3832428-3833457:-
Coord C1 exon
chr3:3833389-3833457
Coord A exon
chr3:3832544-3833388
Coord C2 exon
chr3:3832428-3832543
Length
845 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGAG
5' ss Score
4.86
3' ss Seq
TGTGGCCTCTGTCATTTCAGGTG
3' ss Score
10.76
Exon sequences
Seq C1 exon
ATTTTGGCTATGGAAAGGGGAAATGTACTAAACAAGGCCCGTCGGGAGCCCATGAGACGCGCTTTGGAG
Seq A exon
GTAGAGTAGCTCAGTGCTTCTTCTTTTCTTCTTCAGACACGGTGCCAGGCAGTGGTCTGGCCATGGGCTTTCAGGATGACAGAGTTTAAGGGGGTATACCTGGAGCCCAAAAGAATACTGGAGATGGACGCCCAAGGATTGAAGACTGAGTGTGAGGGCAAAATAATTTATAATGTCAGAGGTGCCTGGGAGGTGGAGAGGCAGCAGGATACAAGTCACACAGAAGCCCACTTTACTCAGGCTGGCACCCACATAAGATGTGGATGTTATGAGACCCACATAAGCAACTGAGTGTGGTAGGTGTGGAGGTAGAGGCTGGTCAACTAGGGTACTTGGAGGAAAGGTCGGAGGAAGGGATGGCATAGAGCAGATCTGGCATCTCAGGAGCTTTGCTTTTTTTTTTTTTTTTTCTTTTCTTTTCTTTTCTTTTTTTCGGAGCTGGGGACTGAACCCAGGGCCTTGCGCTTGCTAGGCAAACGCTCTAACCACTGAGCTAAATCCCCAACCCCCTCAGGAGCTTTGAATCCCCTACAGGAGTAGCCTTCAGTCCACACTGAGTGTATGGAGTGAAGTCAGCCTGGGCACGTGACTCAGAGGTAGATAAGTTACCTCATTGTGGACGGACCCCTGGACTTGATTTTCGGCTCAGCATCTTTTGTTCTAAGGAGGCAAGGGTTGTCTCAGGGCAACCACATGGTGAAAACCTGCCAGAGTGGGCCTATTCTCCAATCTGGCTGGGCAGCTCACCTCCCTGTTCTGCAGTGTTCTTTGAGTCACAGTTGAAGTGTGATGGTAGCACACGATGCTGGGCCCTCTCACAGTCTCTGTGGCCTCTGTCATTTCAG
Seq C2 exon
GTGACAAACTTGAAGACCTTGAAGAAGCCAATCCATTCTCCTTCAAAGAGTTTTTGAAAACCAAGAACCTCAGCCTGTCAAAAGAAGACACAGCCACCAGTCGAATTTACCCGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018876:ENSRNOT00000061669:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.792 A=NA C2=0.359
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
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:
ATTTTGGCTATGGAAAGGGGA
R:
CGGGTAAATTCGACTGGTGGC
Band lengths:
182-1027
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]