BtaINT0129890 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001352 | SDCCAG3
Description
Bos taurus serologically defined colon cancer antigen 3 (SDCCAG3), mRNA. [Source:RefSeq mRNA;Acc:NM_001046140]
Coordinates
chr11:103914134-103914762:-
Coord C1 exon
chr11:103914650-103914762
Coord A exon
chr11:103914452-103914649
Coord C2 exon
chr11:103914134-103914451
Length
198 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGC
5' ss Score
9.37
3' ss Seq
CACTTCCCCGCCTTCTCTAGGAA
3' ss Score
9.99
Exon sequences
Seq C1 exon
ATGATAAACTTGGAGATCTGGAAGCGGCAAACCCGTTCTCCTTTAAAGAGTTTTTGAAGACCAAGAACCTGAGCCTGTCGAAAGAGGACACCGACAGCAGAGTTTACTCACAG
Seq A exon
GTATGCCTGAGGCCGCGTTCGCAGCGACCCTGGAAGCCCTCCGGACGTCTCTCCTGAGGCGCGCGGGACAAGGGACGAAGCGGGGCAGTGAGGAGTTCAGGCCCACCAGGCTCCTCTCTCTCTGTGCCAGCAGCAGACGTCTGGGAGGGACGGCCTGCAATGGCCCCAGTCTAAGCATCACTTCCCCGCCTTCTCTAG
Seq C2 exon
GAAGCCACGAGGCACTCGCTGGGACTCGACCGCACCTCCCCAGCTTCCCAGACTGTGGGCTATGGCCTGGAATATCAGCAGCCATTTTTTGAAGACCCAACGGGGGCTGGCGACCTCCTGGACGAGGATGAGGATGAGGAGGACGGGTGGAACGGGGCCTACCTGCCGTCCGCCATGGAGCAGACGCACTCCTCCAGGGTGGCCGCCAGCACGTCGCCCTGCAGCACGTACGTCTCCTTTTTCTCCAACCCGTCGGAGCTGGTGGGGCCCGAGTCTCTGCCCCCATGGACGCTGAGCGACTCCGACTCTCGCATCTCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001352:ENSBTAT00000055628:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.329 A=NA C2=0.731
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF130941=CENP-Q=PU(6.4=12.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
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:
GAGATCTGGAAGCGGCAAACC
R:
CCGTCCTCCTCATCCTCATCC
Band lengths:
247-445
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development