BtaINT0129892 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001352 | SDCCAG3
Description
Bos taurus serologically defined colon cancer antigen 3 (SDCCAG3), mRNA. [Source:RefSeq mRNA;Acc:NM_001046140]
Coordinates
chr11:103913433-103914132:-
Coord C1 exon
chr11:103914043-103914132
Coord A exon
chr11:103913507-103914042
Coord C2 exon
chr11:103913433-103913506
Length
536 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGT
5' ss Score
9.07
3' ss Seq
AGGATTTTCTTTTTCTGCAGCTG
3' ss Score
8.41
Exon sequences
Seq C1 exon
CCGACGGGGAGCCCCAGCGCTGACTTCACAGCCCACGGAGAGAGTCTGGGGGACAGGCACCTTCGGACACTGCAGATAAGTTACGAAGCA
Seq A exon
GTAAGTGAGGTGGGGGTTGTGTCGGCGCCCCTCCCTGGTCACTGCTCGTGCCTGAGCAGCATTCTTGGAGGATGCCGGAGCCCCCAGCGTCCTCCATGGCCTGGGGTTTGGGCTCCAAGCACGAAAGGCTGTGGTGTCGCAGCTGCGGCAGCATCCCCGTGCTTACCGTGTCGGCGCCCGGAAAGACCCAAGGAGGACTGGCAGAGGACTGCCGGGGGGCCAGTCTCCAGCATGAACGGGGGCAGGGGGAGACCCTCAGAGCGCTGCCCCTCAGAAAATGGTCCACTCCAGGCAGCGGTTGAGGACAGCTTGCCTGGTGAAAAGATTACAGTCGCTTAGAGTTATTCTGAGTAAAAGTGGAGTCTGTGACAGGTTCTAAAAAGCAGACACTTCGGTTCTCTCTTTCTCTATGTGGACTATAGAGTGATACTCTGGAATGTTTTTGTTTATTAAGAAGTTCCAGAGCCAAACTGTGAAAATGAAGACTCCTTTTGAGTGAGACACTGAGTTCTAATAAGGATTTTCTTTTTCTGCAG
Seq C2 exon
CTGAAAGATGAGAATTCTAAGCTAAGAAGAAAGCTGACTGAGATTCAGAGCTTCTCTGAAACTCAAACAGAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001352:ENSBTAT00000055628:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.533 A=NA C2=0.160
Domain overlap (PFAM):
C1:
PF041569=IncA=FE(18.0=100),PF079026=Gp58=PU(16.2=93.3),PF131661=AAA_13=PU(13.1=63.3),PF0076914=ERM=PU(10.6=56.7),PF057016=WEMBL=PU(10.1=50.0),PF0026115=Tropomyosin=PU(10.3=40.0),PF149321=HAUS-augmin3=PU(8.1=40.0)
A:
NA
C2:
PF041569=IncA=FE(14.9=100),PF079026=Gp58=FE(13.9=100),PF131661=AAA_13=FE(16.6=100),PF0076914=ERM=FE(14.9=100),PF057016=WEMBL=FE(16.2=100),PF0026115=Tropomyosin=FE(20.5=100),PF149321=HAUS-augmin3=FE(16.1=100),PF107214=DUF2514=PU(16.2=64.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development