BtaINT0129896 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001352 | SDCCAG3
Description
Bos taurus serologically defined colon cancer antigen 3 (SDCCAG3), mRNA. [Source:RefSeq mRNA;Acc:NM_001046140]
Coordinates
chr11:103910385-103912223:-
Coord C1 exon
chr11:103912084-103912223
Coord A exon
chr11:103911382-103912083
Coord C2 exon
chr11:103910385-103911381
Length
702 bp
Sequences
Splice sites
5' ss Seq
TAAGTGAGT
5' ss Score
6.43
3' ss Seq
CCTCTGGGCTTTCATTTCAGGCA
3' ss Score
8.8
Exon sequences
Seq C1 exon
GCCCAGGTCTCTGACTTCAAGCGTGAGAACGAAGCCCTGCGGTCAGGCCAGGGCGCCAGCCTGACGGTGGTGAAGCAGAACACGGACGTGGCCCTGCAGAACCTCCGTGTGGTCATGAACAATGCTCATGCCTCCATTAA
Seq A exon
GTGAGTGCGGGGCCCTGGCCGCTGTCGAAGCTGCAGGCTGGGGGGCGGGCTCGTGACCCTGTTCACCCCAGGGTCATGGGAGGCAGCCTGGGCCAGCAGCCCCTCCCGGTCCACATGGGGATAACTGATAACCATTCTCACCTGGGAGGCTTGAGGGTTAGCATCAGGCAGGTCTTAATCGCCTGCAAGACGTCTACCAAGATTTTGGGTGAAACAGGATGACAGTACTGTCTCTCTCATAAAAACACACGAACTTGAACAGGGCTCCCGGGAGGCGTCCTGGGCTGGCGTCCTCTGTCTCCCTTGAGCGCAGCGGGCAGCGGTGTCCAGCCTCAGCCACAGACAGTGAGGCCCGTCACCTTTAAGCTGAACACGTAGTGTGTCTGGAGAGTAAATCTGACGTTGAACAAACTGCGGCTTTTGCTCGAGACCTTCTTTGCTTTAACGCTCTGGGGTTTTTGTTGTGTGTGTTTGTTTGGGGGTTTATGGGGAGTATTTTTTGTGGGGCGGGGGTGGGGTCAGGATGCACCACGCAGCTTTTGGGTTCTTAGTTCTCCAGCCAGAGCTCAAACCTGTGCTCCCTGCAGTGAAAGCGTGAAACCCTAACCCCTGGGCCACCAGGGAAGTCCCTGTGCTTCTGTTACTGCCCCGGAGCGATTGTATTAATAGAAGCCATCCGTCACCTCTGGGCTTTCATTTCAG
Seq C2 exon
GCAGCTGGTTTCTGGAGCTGAAACGTTGAATCTCGTTGCTGAAATCCTTAAATCTATAGACAGAATTTCTGAGATTAAAGACCAAGGGGAGGAGTCGTGAGAGCCACGGAGGTGCTTCCAGCTCCCAGCTCTGTTTACATCCTGAAACCACTTCCCGACGGATTCCAAGCTGCCGCGGCGTCTCTGAGTGTGCAGACTTCACCCACAGTAAAGCTTTATCCCAAGACACTAACTTCGTGACGTGCGGCAGTGTTATTAGCCACACACGGGGCCGCACCTGCGCTTCTGCGTAGCCTTTCTAGCTGAGCTCCACACCGCCTCGTAGACGCTGATCATCTATTTGAAGGCAATTCTATAAAAGCCAGTGATTTTTTTTTTAAGTTAGTAAACGAAAGCAGCGGTTCTGTAGTGTTTCCGTCGTCACTGCAGCGCTCTAGCTGTAAGATGAGTTCCGTTGGCCGTCTTTCTTTTGTCAGTAGAGACACACTACGCGAGCCGAAAAGCACGCCCTCGCCTTGGACAGGGACGTGTGCCTTACTGCCCTCGCTCAGCGTGCCCTGGCTTGCGGTCTGCTCCCTCAGCTTCTGGCAGGGGAGGGCTCTTGCTTGGTGGTCTGAGCACAGGCGCCCTGCACGGCGGCCACTGTTGTCCCCCAGGGACCAAGGTCAGCACAGGCATTCCACAGCCGGACGCGGGCTAAGAGCATCTCTTCACGGGCCTTCGCCTGGGAGCGCTGTGGCTGGAGGGCTTGATAGGCGTTTCCAGCGGCAGCTTGCGCAGCGACGTGCAGGGTTCAGGGACGGGAAGCGTGCGCAGACTCCCCAGGTCAGCTTGAGGGCCCCCAGGGTGCCTTCCAGCCCCTCCTATCGGAGGAGCTGTAACACACACTAGATGCCTTTTGTGCTCTTTTCCTGTGGGTGTTATTTTTTTAAAATAAACGTCCTTTTCTCCTCCTGTTCAAATCGACAGTTTTCTTATTTAATAAACTCTAAAAGTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001352:ENSBTAT00000055628:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.112 A=NA C2=0.083
Domain overlap (PFAM):
C1:
PF041569=IncA=PD(15.5=53.2),PF079026=Gp58=FE(26.6=100),PF131661=AAA_13=PD(28.3=87.2),PF0076914=ERM=FE(28.6=100),PF057016=WEMBL=FE(31.1=100),PF0026115=Tropomyosin=PD(17.1=42.6),PF149321=HAUS-augmin3=FE(30.9=100),PF107214=DUF2514=PD(23.2=48.9)
A:
NA
C2:
PF130941=CENP-Q=PD(14.7=88.2),PF131661=AAA_13=PD(5.1=23.5),PF0076914=ERM=PD(17.3=91.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGAACCTCCGTGTGGTCATG
R:
TGGAGCTCAGCTAGAAAGGCT
Band lengths:
356-1058
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development