BtaINT0078141 @ 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
chr13:20277440-20279303:+
Coord C1 exon
chr13:20277440-20277529
Coord A exon
chr13:20277530-20279162
Coord C2 exon
chr13:20279163-20279303
Length
1633 bp
Sequences
Splice sites
5' ss Seq
AATGTGAGT
5' ss Score
7.8
3' ss Seq
CTTATTAGTCTTTCTTTTAGTCC
3' ss Score
4.36
Exon sequences
Seq C1 exon
GAACTGAAAAATTTGATCCCTAAGTCAGCGGTAGGAACATTATCTGCAAATTCCAGCAATGTGATTCAGTTGATCATCGATGCGTACAAT
Seq A exon
GTGAGTGCATTCTAAGTAAGATCTGTTTTGGGCAGTACCCTGTTGAGAATACTTTGCTTAAAAATAGTAAAACTCCTTTCATACACAATTTAGCAGGCCCCACAAGACAATGTAAAACTTGTATGTAAAATTCTGTATGTGGAGGAAAAACTCATTTTCTTACAAAAATGTGTTTGCAAGGCAAAATAAAAGGCATGGCGGGGGCTGGATTTCTAAATTCTGTTTGAATGTCATTAAGTAATAAGTCTCCTTTTTGGAAAACAAGTATGAAACAACTTTCATTTAGATTTATAGGATTACCTCAGTCTTCTGTACTTCCCTTCATTTTATAGATTCATTGATTTTGATGAATTGTGCCAGAAAAGCCTTTTATTTTTTTCTAATTCTTCTCTTGCCATATTTTCAGGGTACATAGTTCTCTGTTCTCAAGTGGTACACACACAGTCATATGTGCATGTACTATAAAATATATATGAATGCATACATGACTTATTAAAGTAAGATTTATAAGATTTTTACCCCATGTGGAAGGAAGTTGAAATTAAAAGAGGAATTGTTCATCTCGAGTTTAGTTCCGAGTACTTTAGGGATACTCATTAAGCCTTGGTCAGTAACTGTTGTAAGTCATCAGAGGCCTTTGTAATACAACTGTAACCATCCTGTGCTGCATACACCAGCTCCAGCCCTTCGACAAGTTGAATTTTATTTTCTACTTCATGCCAGGGGGTTACAGAATGTTTTGGAAAGACCCTACTCAGATTTTTACAGACTTTCTAGATTCTGGTTTTTCCCTGTCACCCCCATAGTCGTTCTGTCTTTACAGCATATCTTAATGCTTTCCTAACTCCATCTGTTGGGCTTCCCTGGTGGCTCAGAGGTTAAAGCGAGTGGTGTGACCAGGACTGAGCTCTCCGCTGCAGCCTTCTCCATTTGTCCTGCGCCCTCTGCTGTTCTACAAAAGCACTGGCTTGAATCCTCCCACTCTGGGTTTTCTTTCTTTGAGGGAGTGGGGGCAGGCCTGCAATGGCCCCTAAGCAGATTTATTTCCAGCCTGTGTAGTAGGTTATTTACCTCTGTCCTTCGTGAGCTGAGGCTTCCCTGATGGCTCAGACGGTAAAGAATCCGCCTGCAGTGCAGAAGACCCAAGTTTGATCCCTGAGTTGGAAAGATCCCCTAGAGAAGGGAATGGCAACCCACTCTAGTATTCTTGCCTGGAGAAATCTATGGACAGAGGAGCCTTGTGGGCTATAGACCATGGGGCTACAAAGAGACATGACTGAGCGACTAACGCTAGTGAGCTACAAGTGGCAGGGCAGAGGAGAGTGTGTTGCCAGTGGGGAAAGAAAGTATTCTTTGTTCTTAGAACTCTTCATAATTAATATTAGGCCTCTGTGCTGTGTCATCATTAAAATTTTAACTAAATACTCTTTTCAGTTGTGTACATTATTTTGAATAATTGGTTATTTATTTGAGCCCATTTCTCTGGGTTTTGTGTTTTCTAGTCACTCAAGATTAGGCTTGCAGTATTTAAATAATACTGTTTTAACAGCTCATTTTATCCACTGGATTTATGAATTCAACTTGTTTTATAGTATCATTTGTTTGCCTTTCCTCTTATTAGTCTTTCTTTTAG
Seq C2 exon
TCCCTTTCTTCAGAAGTCATTTTGGAAAACAGCAAATTGCCGGAAGGAGTAACAATAAATTACAAGTCTTACTGCAAGAATGGGGTGAATGGAACAGGGGAAAATGGGAGAAAATGCTCTAATATTTCCATTGGGGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015910:ENSBTAT00000056716:9
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=FE(6.7=100)
A:
NA
C2:
PF0036213=Integrin_beta=FE(10.7=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:
GAAAAATTTGATCCCTAAGTCAGCGG
R:
TCCCCAATGGAAATATTAGAGCA
Band lengths:
222-1855
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development