BtaINT0078128 @ 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
chr13:20279474-20281298:+
Coord C1 exon
chr13:20279474-20279673
Coord A exon
chr13:20279674-20281059
Coord C2 exon
chr13:20281060-20281298
Length
1386 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
ATTTTGGATTCTTTGTTCAGGTG
3' ss Score
7.2
Exon sequences
Seq C1 exon
GTTCAGTTTGAAATTAGCATAACTGCAAATAAATGTCCAAATAAGAACTCTGAAACCATTAAAATTAAGCCTCTGGGCTTCACTGAGGAAGTGGAGATTATCCTTCAGTTCATCTGTGAATGTGAGTGCCAGGGTGAAGGCATCCCAGGAAGCCCCAAGTGCCACGACGGCAACGGGACCTTCGAGTGTGGGGCCTGCAG
Seq A exon
GTGAGCGGGGGCGCGCACGGTCTCGGGGCATGGCAGCTGGGACATCCGGAGGCCGTCTGAGCTTCCCGGAATCTCTGTGGGAGCAGATGAATTACTCTGCCAACTACTGTTGCTCACCACAAGATCAATTTGTTGGTCTTGTGTGTGTGCTTTATAGAAAGCTCTTCTCTGCCTTTTTTCCTTTAGGCAGACTACTTTTTATTCTAAAATAAAAGCTTTTGTAGCCATCTAAGATGTTACTTAACAAATGTTTATGGTAGCATTTGGGTTTTTCTCTCATGATAGCAATCTGAACTCTGTAGAGCTCAGTAAGCTTATAGAAAATAATAGTGATTTTATATGGGAACTGGAATTAGGAATTAATAAAGGATGTTCACTTGTTATTACATGTACTTCTGCATTGTTGGAATAATTTTAATTCATATATTTGTAAAATTAAGAAAGCACTATTTTTAGAACATAGAATCTACTACTAACAGAACTTAAGTCAAATTAGTTTTAATTTTTATACTATAAATCTTCCTATTTCATCTTTCTCCTATTTTTTTAGAACAGGAGAGAAGACTATTTTGATTCAACTGTCAGCTCCCAAATGACTAGGCTTTGAAGGGTTTTTAATCATGAGGAAAATTAATGACTATTTTGCCATCATTTACTAGCTTTCTATTCTAAACAACAAAATGTTACATTTGTTATTTTCCATGTCATATCCTGAGTTGTATAGATACATTTTTAGTAAAATATTATCTGAAAGATCTTGAAAATGTTTTGCCTTCTTTTTGTGTATTTACCAGATACTGTATTATACCAGTGTGTATAAGCACTATAAAAAGTGTCTGAAAAGTCTGAATCCTTAAATTTATTTTTAAACATTATGGTAGTTACATTTTTAAATGATACTTTTAGTATGGTTTTCAACTTCCATGTACTTTTTGGGCTGTGTTTTTATCAGTTCAGTCGTTCAGTTGTGTGTTTTTATACTTTTTAGTATAAAAATTGGGTATAAACATTTAGTATAAAAATTGGGCAAATAATAGTAAATGTAATATACAGCATATCCTTTGGAAACATACCACACTCTTTAAAAATAAGTTTATCCTTTGTTTCCAAATGTTGTGTTTACCTGTTCATTGCTAGATTGTATTTTCATTTTGATCAGAATGGTTACTTTCCTAAAGAGGAATTTGTTCCTAGGCCCCTGTGTAGACTCCGTGTGGACTTGAATGGCTGTGTGTGTGTGTACACATGTACATATGTACACTTCTGTGACACATATTATATAATTGCAGTCTGAAGATAATGTTTATAGTTTTATTTCCTCTCTTTCTCACCACTTGTTACTTTCAATTCTTTTTGTGTGACTGAAATTTTGGATTCTTTGTTCAG
Seq C2 exon
GTGCAACGAGGGACGTGTCGGGAGACACTGTGAATGTAGCACAGATGAGGTGAACAGCGAAGACATGGATGCCTACTGCAGGAAAGAAAACAGTTCAGAAATCTGTAGCAACAATGGAGAGTGTGTCTGTGGACAGTGTGTGTGTAGGAAGAGGGACAATACAAATGAAATTTATTCTGGCAAATTCTGCGAGTGTGATAATTTCAACTGTGATAGATCCAATGGCTTAATATGTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015910:ENSBTAT00000056716:11
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=0.000
Domain overlap (PFAM):
C1:
PF0036213=Integrin_beta=PD(9.3=59.7)
A:
NA
C2:
PF079748=EGF_2=WD(100=46.9),PF079748=EGF_2=PU(32.3=12.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGGGCTTCACTGAGGAAGT
R:
AGCCATTGGATCTATCACAGTTGA
Band lengths:
356-1742
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development