BtaINT0078127 @ 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
chr13:20279163-20279673:+
Coord C1 exon
chr13:20279163-20279303
Coord A exon
chr13:20279304-20279473
Coord C2 exon
chr13:20279474-20279673
Length
170 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGT
5' ss Score
9.81
3' ss Seq
CTTCTTGTTTTCCTTTTAAGGTT
3' ss Score
12.5
Exon sequences
Seq C1 exon
TCCCTTTCTTCAGAAGTCATTTTGGAAAACAGCAAATTGCCGGAAGGAGTAACAATAAATTACAAGTCTTACTGCAAGAATGGGGTGAATGGAACAGGGGAAAATGGGAGAAAATGCTCTAATATTTCCATTGGGGATGAG
Seq A exon
GTATGTTTCATGAACATTTTTCTGAAGTAAAAGAAAAAGCTTACTTGTTTATAAGCAATTTAGCTTATAATTTGAGAAACAGTTAAATATAACTTGAGTAGCTTTTTGAAAAATTTTTAGTAGATTTAAATTGCTTAGTTTTTAACTTATCTTCTTGTTTTCCTTTTAAG
Seq C2 exon
GTTCAGTTTGAAATTAGCATAACTGCAAATAAATGTCCAAATAAGAACTCTGAAACCATTAAAATTAAGCCTCTGGGCTTCACTGAGGAAGTGGAGATTATCCTTCAGTTCATCTGTGAATGTGAGTGCCAGGGTGAAGGCATCCCAGGAAGCCCCAAGTGCCACGACGGCAACGGGACCTTCGAGTGTGGGGCCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015910:ENSBTAT00000056716:10
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(10.7=100)
A:
NA
C2:
PF0036213=Integrin_beta=PD(9.3=59.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAAAACAGCAAATTGCCGG
R:
CCCTGGCACTCACATTCACAG
Band lengths:
253-423
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development