BtaINT0078236 @ bosTau6
Intron Retention
Gene
ENSBTAG00000009080 | ITGB6
Description
Bos taurus integrin, beta 6 (ITGB6), mRNA. [Source:RefSeq mRNA;Acc:NM_174698]
Coordinates
chr2:36315952-36316950:+
Coord C1 exon
chr2:36315952-36316086
Coord A exon
chr2:36316087-36316532
Coord C2 exon
chr2:36316533-36316950
Length
446 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
ATTAGTATTTCCTTTTCCAGGCT
3' ss Score
7.54
Exon sequences
Seq C1 exon
GAACTGCGGTCTGAGGTGGAGCTGGAAGTGTTAGGAGACACGGAAGGACTAAACCTCTCATTTACAGCCATCTGTAACACCGGGATCCCCGTTCCACACCAAAAGAAATGCTCTCACATGAAGGTGGGAGACACA
Seq A exon
GTAAGTAGAGATCAATAGATCATCTGAAAAGTCATTCAGATGATCTGTCAGAAGTTACCTTAGTGCACTAAAGCTGGACTTTTCCTTTCAAGAATTTCAAAAGCGATTTTCAAAGATTTCCTAATAAATGCTTTCGGGAAAGCTGATCCCCATGGGCTCTGTATACTCCAGTGCATTTTGATGGCTTGTTGCTCTTGCCGTTTAGTCACTGAGTCATATGTGACTCTTTTGTGACCCCGTGGACTGTAGCCCACCAGGTTCCTCTGTCCATGGGGTGGCCTGGCAAGAATACTGGAGTGGGTTGCCATTTTTTTCTCCAGGGGATCTTCCTGACCCAGGGATTGAGCCCACATCTCTTGCATTAGCAGGCAGATTCTTTGCCACTGAGCCACGAGGGAAGATCATTTTGGTGATTAGAAGAAGATAATTAGTATTTCCTTTTCCAG
Seq C2 exon
GCTTCATTCAATGTGACTGTGAGTTTACCAAACTGTGAGAGAAGGAGCAGGCACATTATCCTAAAGCCCGTGGGGCTGGGGGACGCTTTGGAAATCCTCGTCAGCCCGGAATGCAGCTGTGACTGCCAGAAAGAAGTGGAGGTGAACAGCTCCAAGTGCAACAACGGCAATGGTTCCTTCCAGTGCGGGGTGTGTGCCTGCCACCCTGGCCACATGGGTCACCACTGCGAGTGCGGGGAGGACACGCTGAGCACCGAGTCCTGCAAAGAGGCCCCAGGGCGCCCCTCGTGCAGTGGGAGAGGCGACTGCTACTGCGGGCAGTGTGTCTGCCACTTGTCCCCCTACGGAAACATTTACGGGCCTTACTGCCAGTGTGACAACTTCTCCTGCGTGAGACACAAGGGGCTGCTCTGCGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009080:ENSBTAT00000011972:10
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(10.4=100)
A:
NA
C2:
PF0036213=Integrin_beta=PD(9.2=27.9),PF079748=EGF_2=WD(100=25.7),PF079748=EGF_2=PU(32.3=7.1)
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:
TGAGGTGGAGCTGGAAGTGTT
R:
CAGTGGTGACCCATGTGGC
Band lengths:
351-797
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]