BtaINT0078256 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018993 | ITGB7
Description
Bos taurus integrin, beta 7 (ITGB7), mRNA. [Source:RefSeq mRNA;Acc:NM_001105365]
Coordinates
chr5:26964403-26966551:+
Coord C1 exon
chr5:26964403-26964606
Coord A exon
chr5:26964607-26966349
Coord C2 exon
chr5:26966350-26966551
Length
1743 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAAG
5' ss Score
5.75
3' ss Seq
CGCCTCCCCTTGCCGCGCAGAAC
3' ss Score
7.72
Exon sequences
Seq C1 exon
ACCATGGTGGCTTTGTCAATGGTCCTTGTTTTCCTGCTGGCCCTGAGCAGAGGTGAAAGTGAGTTGGACGCCAAGAGCTCATCCCCACAGGAGGCCACAGAGTGGAGGGATCCCAATCTGTCCCTGCCAGGGTCCTGCCAGCCAGCTCCCTCCTGCCAAAAGTGCATCCTCTCACACCCGAGCTGTGCATGGTGCAAGCAACTG
Seq A exon
GTAAAGATGGGCCTGTGACCTCTGAACCGTGTGTGTGTGTGAATGTGTGCAACCTGGATATACAAGTATGATTGTGTGGGTACATGTGTGACGTTCTGGGTACGCTCTGTAGTCCTGTATATGACTGAGTTTGTGCACATATGACTTCTGTCTGTGATTGCATGTGTGTGGGCACACACATGCATGCAAGAGTCCTCTGCATACATGTTTGTCTGCATCTGTGTATCTGTGTATATATGGAGAAGACTTGTGACCTTAAACTTGGAGGAAGCATGTTCTTACTGAACTCTTGTTTGTGTATAGCGAGAGGGATCTTTTGTGGGTATATCCATGAGAAAGTGTATTTGTCAGCTTGGGGCTGTCAAAATACCATAGACTGGGGTGGGGGGGGCTTAAGTGACAGGAATTTATTTTACAAACAAATTGTTTGAGGATGTGAAATCCCAGATCAAGGTGGTAGCTGATTCAGTTCCTAGTGAGAGCTCTCTTCCTGGCTTGCTAATGGGCTGCAGACAAGCTCTCTGGTGTTTCTTCTTATAGGGATCTAATCAACAGATCATGAGGGCTCTACTCACATGACCTCATCTAACCTTAATTTATTCTCTAAGGCCCCAACTCCACATACTATCATGTTGGGGGTCAGTCCACTGCAAAAGTGTGTGATTGGGTTTCTGGATCTGGGTTGGGGGTGGAGGTGTGTTCCTGGGTATGCAGCAGCCTATGACTGGGAGGGTAGGCTGGAAGGAGCTGGAAGCCTATGGGCTTTGGGGCAAAGGCTTGAACTACCTAAGTGGCAAGAAGGATGTGGGGGGTGGGGGAGAGGGTGTCTTCCTGGCTGGTCAAACAAAGCTGTTCTTTGTTCATGCCTTAAAGAGACAGGGCTCTGGTGTAGCAGAGCAAAAGGGGTGCCTGAGCTGGGGGGATGGGGCAGAACCGTCTCACAGGAAATGGGGAGTTAGATGAGATAAGAAAGGCGGGCACACTCATGGGGGGAAGACAGAGCTCCAGAGCTGAGTGGATCCAGGAGAAAGGCACGTAGTGAATCTGGGAGGCCTGGAAGGGGAAGACACAGTCAGTGGGAGGCAGAGAGCAGAGGTGCCAGGCCAGAGGAGCCAGGCAGGGACTCTTGGGCCAGCTGGATGCGAGTCAGTCTCCTCCAGTCCCCAGACCAGAGCCTGGCTGGCACCTGGGCCAGCTGAGAAGCTGCTCTAACCATTTCCTTCCCCTGTGGCTCCCCAGCCAGTCCCAGGGTACCAGACACACTGAGGAGAAGGGGGTATTCTCTTCTGTCCCTATCGTTTCCCTTCCCAGAAACTGTCTTAATCTGACCCCCTTCCTTTTTTGGCCTGAGTTTGCAGCAGGGAAGGGCGGGGCGGGGCGAGGGTGGACTAGGAGGACAGGTTCTTCCTTTTTTAATGGTAGTGAGGTCCCTAAGATCTCAGCAGGAACTCTGTCCTGCTGTGGGAGGTGAGAGGTAGGTATCTGGCGGAAAGGGGGTGTCGAGATGAGGGTAGGAGAAGGGAGATGCTGTAGGAAGTGGGCTCTGGACAAGGAAGTAAGTACGAGGTTCGAGGGTAGCTGTGGAAGGAAGGGAGGGGAGGGAATTGGGGGTGGGTGCGGGGCTCAGGGAGTTGCCTAACAGGGGAGGGCTTGGAAGTGGCCAGGACGGCAGGGTGGTTCTGGGAGCCGGGCTGAGGGTTTCGGGGGATCAGGGTTCCCCACGCGCCTCCCCTTGCCGCGCAG
Seq C2 exon
AACTTCACAGCGTCCGGGGAGGCGGAGGCGCGGCGCTGTGCTCGGCGAGAAGAGCTGCTGGCCCGGGGCTGCCTCCCGGGGGAGCTGGAGGAGCCCCGCGGCCGGCAGGAGGTGCTGCAGGATGACCCGCTCAGCCAGGGCACCCGCGGCGAGGGGGCCACCCAGCTGGCGCCGCAGCGGGTCCGGGTCACGCTGCGGCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018993:ENSBTAT00000025279:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.299 A=NA C2=0.471
Domain overlap (PFAM):
C1:
PF0036213=Integrin_beta=PU(4.0=25.4)
A:
NA
C2:
PF0036213=Integrin_beta=FE(15.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCATGGTGGCTTTGTCAATGG
R:
CCTGGCTGAGCGGGTCATC
Band lengths:
342-2085
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]