BtaINT0078139 @ 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
chr13:20276173-20277160:+
Coord C1 exon
chr13:20276173-20276328
Coord A exon
chr13:20276329-20277064
Coord C2 exon
chr13:20277065-20277160
Length
736 bp
Sequences
Splice sites
5' ss Seq
TACGTAAGT
5' ss Score
9.27
3' ss Seq
TTTATTACTTAATTTCTTAGGAT
3' ss Score
8.42
Exon sequences
Seq C1 exon
TCCCTGATTGGTTGGAGGAATGTGACACGGCTGCTGGTGTTTTCCACGGATGCTGGGTTTCACTTCGCTGGAGATGGGAAACTTGGTGGCATCGTTTTACCGAATGATGGACAGTGTCACCTGGAAAATGATGTGTACACAATGAGCCATTATTAC
Seq A exon
GTAAGTGCTTAGCGCCTTACATATTCAGTGGATTTGGGTTTTTAGAGTATTATGGGTAATGGGCTTGTGGGTTTTTCAGGATTGGGGTTTTGTTATTTTGGTAAGTTGGGCCCTGACCTAATGTGCAGGAAAGCTTTGTTGCTGTTCTGATGCTGTGGCTTTGTGCCTGCTTCTGCGTAGCTGAAGGCCTGGTGGTGAAGGGAGCTGCTGACTCCTGGCCCTGCACCCCAGCCCAAAGCTCTGTCTCCTCTCACTCGGTCCATCAAGGAGTACCAAGTTTGATACTATGTCTAAACAAATCATTTGTATAGTCTTACACTCCTTGTCTTATTTATATATGATTTAAGAAAGTAGGCATCCTGCCTCTACTGAAAATAAACATGGGCAGTTTATTCAAGGTCTGCAAGAAACCTAAACCTTGCTGAATCTTGGTCTTTTTCTTAGTGATAATATAACCTTTAATTATGGCAATTCTTCAATTTCATTGTTCTGACATTTAATATACATAGATAATCTTTTAAAAATCTTTTTTATTGAAATTTTTATGCACACTAAAGATAAAAAAGGATCAGAAACCCACTAGACAGCACCTAGTTCAGCAATAATTTGTGTTGTTTCAGGCAGTCTTGTGTAAGTAATCCAGATATATCTGCAAATCATTATTTTCAGAAAGTTTTGAAAAACTGGAGTATATTGGATATAATTACATACTAAATTTTATTACTTAATTTCTTAG
Seq C2 exon
GATTATCCTTCTATTGCTCACCTTGTCCAGAAACTAAGCGAAAATAACATTCAGACGATTTTTGCAGTTACTGAAGAATTTCAGCCTGTTTACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015910:ENSBTAT00000056716:7
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(11.8=100)
A:
NA
C2:
PF0036213=Integrin_beta=FE(7.2=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:
CCCTGATTGGTTGGAGGAATGT
R:
TTGTAAACAGGCTGAAATTCTTCA
Band lengths:
250-986
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development