BtaINT0078138 @ 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
chr13:20273947-20276328:+
Coord C1 exon
chr13:20273947-20274185
Coord A exon
chr13:20274186-20276172
Coord C2 exon
chr13:20276173-20276328
Length
1987 bp
Sequences
Splice sites
5' ss Seq
GGAGTGAGT
5' ss Score
6.05
3' ss Seq
GAAATCCTTTTCTTTTCAAGTCC
3' ss Score
5.89
Exon sequences
Seq C1 exon
GGTTTGGTTCTTTCGTGGAGAAAACTGTGATGCCTTACATTAGCACAACACCAGCTAAACTCAGGAACCCTTGCACAAATGAACAGAACTGCACGAGCCCATTTAGCTACAAAAATGTGCTCAGCCTTACTGATAAAGGGGAAGTATTTAATGAACTTGTTGGTAAGCAGCGCATATCTGGAAATTTGGATTCACCAGAAGGTGGCTTTGATGCAATCATGCAAGTCGCAGTTTGTGGA
Seq A exon
GTGAGTGCATTCTTTCTCTACAGGGGATATTATTTGTGTGGAATTTAAGTGTGATTTTTCTGTCAGAAAATATTACCTTAATTTCTGTACTATACTGATTAATCCCTTAAATTCCCTCCCAACTGCAAGTGGTTTAAAAAAAAGCATAGTTAATCTGGGTTTTAAAAGCCAAAATGCTCACCATTTGAAACAGTGGGGCAGCGTAGCTTTAGCTGGTGTCCTGGGTTTTTTAAGGAGGCTCAGGGTACCCTGGCTTTCAGCTTTGTGACTGAGATGGTATTAGGGTTATCTGAGACGTCACCAGGAACATTAAAAGTGCTCAAATAGATTGTGTGTCAGGCACCATTTTCCTTTGGTTAGTTTTCTTCTGCTTATCTTTGAGAGGCATCTTCCCCATGTCTTAGTAATTTAAAAAGAAAGTTTTAAGTCCTAGTGTGAAAGCTGTATATATTCTGAGAAGTCATATAATGTTTGCAATTTTAATTAGAAGATTTTCAACGACAGTAAGCTGATCCTCCATTGGACTGGTGCTTAGAATTTTTGACTCATTTACCAACCCAAAATTTTAGGTGACCTTTTAATGATGTAGCTGAGGACAGAAGTAGAAAACACTGTGAGCTAGATGAAGTTTTATCTGTCTCATTTCCCCCCCCTTTTTCCTTACAGTACCCCTGTTCCCTAAAACACCTTTCTCTTCCGGATGCTTCTTAATGGTTACTTTTCAACCAAGTTTTAGTATGCTCTTTGATACCCAAGATGATGATATAATACAGTGCTTGAGATAACAGTCTTTAGACTATTAGGACAAAGCTTCAAATGTTCCCATCACTGCTCATCCACTAGGCAGTTTCCTTCTCCTTAAGAGATAATAACAGGTACACCTTAGGAAGTTTAAATACGGTAATCCATAGATAGTGCAAGTAGCCAACAAACAGTTAACAACTGTATTATAGTCAGTCTTGACTTTTCATCAGGGTAGATGCAGTTTAAGGATAGTCTCCACTTTTAAAGGGGAAGAGTAGTTTTCCAGGCAGTGCTTAGCTTGATGCCTGTTTCCTCTCCAGCCATTCATTTGTGATCCCGCTAGAAGCTCATATGGAGAAAGCATTCTTTGCGCTGTCTCTGCCTGAACCTCAGCCTTGAGATTAAAACAGGCCATGGTATCCTGGCCGCTGCTCTCTGCTCCCTGTGCTGACTGAGAGTAACTGTTCCACTTACTTCTCTAAATGCAGAAGAGACATATTCCGGTTGGTCTGCCAGCATGAATAAACTTAATTCTTGCCTTCAAGGATTTTATAGTCTTAGGAAGATATATACAGATGTATGGAGTAAATAAAGACAGATGATTGTAAAATTACCATTCAACAGGATTTTACCACCACTTTAAATTTTTTGCTGAATAAGGTGGAGAATAAAATAAATGAACAAACAGTACTGATGGATTAAAAGGGGTGGAATTAAGCAGGATCAACTCTGAAGAAAATGCTTTTTATTAGAATTAAAAAGGGGAGGCTTTTTTAATATGGTGGCTGATAAAGGGAGTATGTGCTCCAGAAGGTGGAGTAGGTATGGATGGGAAGGGGAGATAACAGTGTTTAGATAAAGTTGGGTGTGGGCTGAGACGTTTTCGTTTATTCATTAAGCACCTAGTAGAGATAAGATGATGCACAAAACCAGATGTGGTCCCTGCCCTGTGTGGAGTGTAGCTACCTTTTAGTGGGGATAAGGACATTGACTTTAAAAGGTAGTTTTTAAAAAAAGAGCTGAGACAGACAGCTAGGCAAGGTGAAGTGTTACAGTGAGGCAGGGGCGTTTTATTCAGCGGGCTCAGTGCCTTTATCAGCGAGGATGTTATTAGCATTGTGAAAAGAGAAAATACAGAATTAAGTTGAAAGTATAGTGGTAGCCTGTATAAAGATTAAAAGATTTAATCTTTGCTGAATTTCTGTAGGTAGTATTTTAAAACTGAAATCCTTTTCTTTTCAAG
Seq C2 exon
TCCCTGATTGGTTGGAGGAATGTGACACGGCTGCTGGTGTTTTCCACGGATGCTGGGTTTCACTTCGCTGGAGATGGGAAACTTGGTGGCATCGTTTTACCGAATGATGGACAGTGTCACCTGGAAAATGATGTGTACACAATGAGCCATTATTAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015910:ENSBTAT00000056716:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.037 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0036213=Integrin_beta=FE(18.3=100)
A:
NA
C2:
PF0036213=Integrin_beta=FE(11.8=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:
TCGTGGAGAAAACTGTGATGCC
R:
TCCAGGTGACACTGTCCATCA
Band lengths:
352-2339
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development