RnoINT0132056 @ rn6
Intron Retention
Gene
ENSRNOG00000018876 | Sdccag3
Description
serologically defined colon cancer antigen 3 [Source:RGD Symbol;Acc:1305930]
Coordinates
chr3:3830916-3832191:-
Coord C1 exon
chr3:3831784-3832191
Coord A exon
chr3:3830990-3831783
Coord C2 exon
chr3:3830916-3830989
Length
794 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGT
5' ss Score
9.07
3' ss Seq
GGAATTTTTTTTCTCTACAGCTG
3' ss Score
8.51
Exon sequences
Seq C1 exon
GAGGCCTCGAGGCACCCACTGGGACTAGACCACAACTCCCCTGTCTCCCAGCCCATGGGATATGGCCTGGAATATCAGCAGCCATTTTTTGAAGACCCAACAAGAGCCAGCAACCTAGAGGAGGATGAAGAGGACGGGTGGAGCAGAGCCTACCTGCCGTCTGCCGTGGAGCAGACTCACTCCACGAGAGCCACGCAGAACTCATCGCCCTGTGGCACCTACCTTTCCTTCTTTTCCAACGCGTCAGAGCTGGCAGGTCCTGAGTCTTTGCCCCCATGGACACTGAGTGACACTGACTCCAGGCTCTCCCCAGCGTCTCCAGCTGGGAATCCTAATGTAGACTTTGCAGCTCATGAAGAATCCTTAGGGGACAGACACCTGCGGACGCTGCAGTTAAGTTACGAAGCA
Seq A exon
GTAAGTAAGGGCAGTGTGGCACCCAACACAGCTGAGCAATGTAGAGAAGAGCTGCAGTCATCTACTTCCTGGGTGGCCTGGGTTCAATGCCTTGGACAAGACAGTTGGTCGTATGATAGCTTGCTGTAGAATTGCCCTGAGGAGGGGCTCGAGATATAGAGAGCTCAGTGGTAGTTTTTCCTAGCACTTGGGGAGTCCTAGGTTAGATTCTGAATGCTCCAAAGTAAGAGAAAAAGGAATTTCTCCATGGAGAGCTCTCCCCTAGGTTGGTTTTGATTGTGCAATTAGTATAGCAGGCAGACATGAGCTAGAATGGATGAACGGTCTATTGGAAGTGCTGGCTAAGAGTCATCCTGCTGAATGCCCCACATGAAGGAAGACTTTGAAACCATAGTCACCTAGAAACATTGAAGTGTGTGGCCACAAGTCATCTCTGTTAAGGGCTTGGGGGTGTTTCCATTTGACCTGGGGTGTTTATGTTCCAGAGCTGGGCATAGACGTGCACAACTGTCATCCCAGCACTTGGAAGGTGAAGGCAGGGGGAACAAGAGTTCAAGGCCATTCTTAGCTACATAGGAGTAAGTTAGAGGGCAAACAAGGCTGCAGGAGATGCTGCCTCAAAAAGATACTTCATGGACAAACGGGATGTGTCTTCATGGGGCCAGCCCTGCCCTGCCCCGAATGCTAAGGTTCCACCTCCAGACCAACAAAAGAAAATATTCCAGGACAGAAGTATGTTCCGCTTATGAGGGAGACATACTGTGTGTCTAATGAGGAATTTTTTTTCTCTACAG
Seq C2 exon
CTGAAAGATGAAAACTCTAAGCTCAGAAGAAAGCTAAGTGAGGTTCAGAGCTTCTCTGAAACTCAAACAGAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018876:ENSRNOT00000061669:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.750 A=NA C2=0.440
Domain overlap (PFAM):
C1:
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)
A:
NA
C2:
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)
Main Inclusion Isoform:
NA

Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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:
AGAGCCAGCAACCTAGAGGAG
R:
AGCTCTGAACCTCACTTAGCT
Band lengths:
358-1152
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]