BtaINT0078136 @ 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
chr13:20271509-20273376:+
Coord C1 exon
chr13:20271509-20271731
Coord A exon
chr13:20271732-20273205
Coord C2 exon
chr13:20273206-20273376
Length
1474 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
TCTAATCTCTGATTAATTAGGGG
3' ss Score
5.05
Exon sequences
Seq C1 exon
ACATTTTTACAAGAAGGTATGCCTACATCTGCTCGATGTGATGATTTAGAAGCCTTAAAAAAGAAGGGCTGTCATCCAAATGACATTGAAAATCCTAGAGGCTCCAAAGATATAAAGAAAAATAAAAATGTAACGAATCGAAGCAAAGGAACAGCAGAGAAGCTGCAGCCAGAAGATATCACTCAAATCCAGCCACAGCAGTTGGTTCTGCAGTTACGATCAG
Seq A exon
GTATGGAAATCTGATTCTAGGAGTGCCTTTGGGTCCACTTGAGCTTCCAGACAACTTTATATATGTTTCTGTTGAGAAATGTTGAGTATGTTAACTTTTAGAAATTTTTTGAATTTTTTGCAGGTATAATTTGTCAGACCATGTACCTGACATTTGCCTAATGTCCAAAGTAAATTCTGTTAAAGATTCAGAAAGTATTATTAATAGATTTAGTGGGTTTTTCAAAAATAAAAATATCCATCTTCTGGTGTAACTATATAACATAAAGATAACATTTTAATCTATTTTTTCCTTTGTTTTTGTACACTACTGTTAAAATATTAAGGTTTTCATAAGAATCTGTAGCAGTCCTGCATCTGGAAAAAAGAAAAAATATGCCCCGTTCTCTTCTAATCTCCAGCCCCTTCCACCCAGGACTCACGTGTGCCCTCCCCACCCCCTCCCCGTTGCCCTCTCTTCAGCCTGGTGCCTCTAGACCTGCTCTGCCAACCTCTGCTGGCACCTGAAACTGCCAGGCCTGATGGACCCTCGGCAGGCCTTTTTTTCCCCTTTATTTAACTCTGCTGTACATGTGATGCCTTTGAGCTTCTTGACATGTTTCTTTTTGGCTTCTGCGATAAGGCTTCTGCTTTCCTTCTTATCTCTTGCCAGTGCCTTCCAGTCTTCTTTCTGTGTCTTTTTTCTTCCTTCCTCTTTGTAATCCACTTAACTGGGCTTTCCTCTCATGGTTTTGAAACCCTTTGTGTGCTATAACACAGACTTTTTTCTCTCAAGCTCCAAACACAGTTACCCAACTGCCTACTAGAAATCTATATAGAGAAAATCTGCAAGTTAAAAACGAAATGACCTTTTACCCAGACCTCTTCCTACTCTCTTCCTACTCGAGTGTTTTCTGATGCATTTCAACTCACACCTCTGGTACATCTCTTCTGTGTCCTTATTGGTTTCATATCTGTATCCTCTTTTTTTCCCCTATAATTTCTTAACAAGTTTGTCTCTTTAATCATCTTAAAACTTTTCATCAGGTTTTCTTAAGTGAAAATCAGATTACTTTATTCATTGCACGCAGTGCATCCCGTAAACAGAGAAGAGTCTCGCTTGACAGCGTCAGTCTCTAATAAAACGCCCGGAGTGTCCTGTGGTGTGCCTGCCTCACCCACCCCATCCAGTTTGTGTTGTTCCTATCTGTTTTCCTTTGTCGTAGTTAGCAACCCACTATTTGCCTGTCTTGCCCACTGTAGATTGGGAATGCTGTCTTTTTCATTATCCCTGGGGCCTGGCATTTTAAATATTTGTGAATAAAAAGAGTACACAGCAATTGATTGAATTCCCTATGGAATGCCCTGGCTTTTGTAAAAACTACGTGAATAATATGGTTTACTCTATAGTGTTGACCTTATCAATCTGATTTACTTGGCTTTTCCATTTGCTTTTGATTGCTGGCAAGCTAGTTTTCTAATCTCTGATTAATTAG
Seq C2 exon
GGGAGCCACAGACATTCACACTAAAATTCAAGCGGGCTGAAGACTATCCCATTGATCTCTACTACCTCATGGACCTCTCCTATTCCATGAAAGACGACTTGGAGAATGTGAAAAGTCTGGGAACAGATTTGATGAATGAAATGAGGAGGATCACTTCAGACTTCCGAATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015910:ENSBTAT00000056716:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.507 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0036213=Integrin_beta=FE(17.2=100)
A:
NA
C2:
PF0036213=Integrin_beta=FE(13.2=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:
GCTCGATGTGATGATTTAGAAGCC
R:
GGAAGTCTGAAGTGATCCTCCT
Band lengths:
358-1832
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development