BtaINT0078137 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015910 | ITGB1
Description
Bos taurus integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12) (ITGB1), mRNA. [Source:RefSeq mRNA;Acc:NM_174368]
Coordinates
chr13:20273206-20274185:+
Coord C1 exon
chr13:20273206-20273376
Coord A exon
chr13:20273377-20273946
Coord C2 exon
chr13:20273947-20274185
Length
570 bp
Sequences
Splice sites
5' ss Seq
TTGGTAGGA
5' ss Score
5
3' ss Seq
ATGTGCGTTTTCCTCCACAGGGT
3' ss Score
13.04
Exon sequences
Seq C1 exon
GGGAGCCACAGACATTCACACTAAAATTCAAGCGGGCTGAAGACTATCCCATTGATCTCTACTACCTCATGGACCTCTCCTATTCCATGAAAGACGACTTGGAGAATGTGAAAAGTCTGGGAACAGATTTGATGAATGAAATGAGGAGGATCACTTCAGACTTCCGAATTG
Seq A exon
GTAGGAATTTTGAGAAAATAATTTTCATTTTTGTAAATCTTAGCTGTTTTATTCTTCACTACATAAATGTGAGATTAGGAGGCTAGGTTTTAGCTTTTTCTTTCTGAGAGGACTGATACTCCTGTCACATGGCTAATGATTTTTCTGCCTCCTTGTTCCTCTCTCACTATAAAAAAGAAAGAAAGAGTCAGTCGTGTCTGACTCTCGGTGACTCTGTGGACTGTAGCCCGCCAGGTTCTTCTGTCATGGAATTTCCCAGGCAAGAATATTGGAATGAGTTTCCATTCCCTTCTCCAGGCGATCTTCCCGACCCAAGGATGGAACCTGGATCTCATGGATTGCAGGCAGATTCTTTACCATCTGAGCCACCAGGGGAGCCCTTCTTACTGGCTGCCATGTTATTTGACACACATTACACCACATAGAGAATAAACTGCATGTTTGTTGTTACAGGAGTTTACTCATTCATTTGTTGATCTTATAAACATGTTGATTACTTAGAGTTGATTTTTTTAATGCAGTTTAACCATCCACCCTCCATCCTCACTGCATGTGCGTTTTCCTCCACAG
Seq C2 exon
GGTTTGGTTCTTTCGTGGAGAAAACTGTGATGCCTTACATTAGCACAACACCAGCTAAACTCAGGAACCCTTGCACAAATGAACAGAACTGCACGAGCCCATTTAGCTACAAAAATGTGCTCAGCCTTACTGATAAAGGGGAAGTATTTAATGAACTTGTTGGTAAGCAGCGCATATCTGGAAATTTGGATTCACCAGAAGGTGGCTTTGATGCAATCATGCAAGTCGCAGTTTGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015910:ENSBTAT00000056716:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.037
Domain overlap (PFAM):
C1:
PF0036213=Integrin_beta=FE(13.2=100)
A:
NA
C2:
PF0036213=Integrin_beta=FE(18.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAGCGGGCTGAAGACTATCC
R:
TGCATCAAAGCCACCTTCTGG
Band lengths:
358-928
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development