BtaINT0129889 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001352 | SDCCAG3
Description
Bos taurus serologically defined colon cancer antigen 3 (SDCCAG3), mRNA. [Source:RefSeq mRNA;Acc:NM_001046140]
Coordinates
chr11:103914650-103916652:-
Coord C1 exon
chr11:103916436-103916652
Coord A exon
chr11:103914763-103916435
Coord C2 exon
chr11:103914650-103914762
Length
1673 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGC
5' ss Score
9.44
3' ss Seq
TGACACTTGGTGTCTTTCAGATG
3' ss Score
9.68
Exon sequences
Seq C1 exon
GAGCGCAAGCAGCGGCCAGCGGCTCGGAGCGGCGGCCGAGCGGCGGGCGACGGAGGCGGGCGACTCGGGCCGCGGCCGGGACGGAGCCGGGGCCATGGAGCCGCCGCTGCCGGGCTGAAGAGGGCTGGCGCCGCGCAGCCCGCGGCGATGGCGGGCTACGCGCGCCGCCCGGGCGTCACCCCGCTGTCCCGGGCCCGGAGCCTCGTCATTCCGGACG
Seq A exon
GTGAGCGGGCGGGGGACGGGCGGGCGGCCGCGGCCCGGCGGCCGCGCTGAGGTCCAGGTGAGGCGGGCGCGCGGGTGAAGTCGCTCTTGTTGTTATTACAGCTCCCGCGTTCTATGAGCGCCGGTCTTGTCTCCCCCAGCTAGACTGTGAGCGCCCCCCAGCCAGGGACCTGGAGTCCCACTTCTTCGGCATTCGGCCGACGTTTATGTGCTATGTGCCCAGTCCGGTGCTAGCTTCCGTGGGAGACACAGGTGAGAGAAGAGCTTCAGGGACCCCGCCCTCCCCGGGGCCGGCGCTGCTTGTGGTACCGCGCGGTAGCGCAGCTCACCCCTCGCGATGACCACTAGCCCCACCGTGTGCCGGGCACTGGGAGTCCCGCCGCCTGGAGCTCACAGTCTGATAGTGGAGAACCCCCCGCCCCCGCCCCCGCCCCGCCAGACAGTTCCGGTAGACCGCAGTAAATGTTGGCTTAGAGGTAGGCCCAGGGTGAGCACAGAAAACCCTGTCTTTCTTCGAGGTGGGAAGGATAAGGGAGCCTTCAGCAGACCAGGCTTCCCATTCCTTGGTCCCCTGCAGCTAGGCGGAGGCCAGCTTTAGTTCCTCCTAATTCTCCCCAGGCGGCTAACACTGCTTGGCCTTCAGGGTATTCGGGGGCATTTAGGTGATTCTGTCGGGGTCTGAGAGCCATTGACCACCCTTGTGGGCGTTCAGGAGGTACCACAAGATCTGCCCCACTGGGCGTCAAACCTATTGGGAGGTATTTCAGAATCACAGATGCCAAGGCCCATGGCAGCAGCCCATGTCCAGAGGCAGGAGCCCATGGGCGTGAGCTTTAAACGTCCTCCAGGCTGTGAGAAACCGCTGCACTAGAGACCCCGTGTCAGAGAAAGCTGGGGTCACAGAGCACTCGTGTGGTCACAGTGGGGTGATGGTGTCTCTCTGCAGATTTTGGCTATGGAAAGGGGAAGTGTGCTAAGCAAGGTCCACCGGGAGCTCAGAACACACACTTTGGAGGTAGAGTAGTTCGGTAATCCTTTGTTTTTCTCTCCACCCGTGTCTCCACGTGCCAGGCACATGCCCAGGGGTGGGGCTGTAGATCTCACAGCGTATAACTAGTATACCTGGAGCCCGGAAGAGCCAGTGGGAGTAGAGCCCCACAGATCTGATCTTCACCGTCAGGTGGAGGGAAGGAGGGCGCAGGGCAGGAGGGAAGTCACGCCTGAGGGGTCTGAAGAGACGGGGGTGGAGCTGAAGTCACAGGAGCCAACTTCACACAGGACTGGCAACTGGGCTGGGCGTCATCGGTGGGCTGAAAGGGCTGCGGTGTGGCTGCCTGGGTCCCCAGGGAGTGGAGAGAGAAGGGAAAGCTGAGGTGAGGCGGGAAGAGGCTGTTCCTGAAGCCTCTGGCTGGGAGGCGGGCCACAGGCGCCTCCGCGCTCCCCACGTGGAGCCCGACGGCAACAAGGCGCAGGGGGCGCGGGGCGGGGCGGGAACCAGGCTCTCGGACGCCCCAGTCGCCCGTCCTGTCAGGCAGCTGGTCATCTCCCGGTGACGGAAAGGACATGAGCATTCCCAGTGTAGGTGGGGTCGCGTTCAGGCGAGGGCAGGGAATAGGAGCTCCCTCTGAGGGCCTTCGAGAGGCTTTCTCCTGTGTGACACTTGGTGTCTTTCAG
Seq C2 exon
ATGATAAACTTGGAGATCTGGAAGCGGCAAACCCGTTCTCCTTTAAAGAGTTTTTGAAGACCAAGAACCTGAGCCTGTCGAAAGAGGACACCGACAGCAGAGTTTACTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001352:ENSBTAT00000055628:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.417 A=NA C2=0.329
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CTGCCGGGCTGAAGAGGG
R:
GTGAGTAAACTCTGCTGTCGGT
Band lengths:
222-1895
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development