BtaINT0073184 @ bosTau6
Intron Retention
Gene
ENSBTAG00000025009 | HOXB9
Description
Bos taurus homeobox B9 (HOXB9), mRNA. [Source:RefSeq mRNA;Acc:NM_001191186]
Coordinates
chr19:38503102-38507053:+
Coord C1 exon
chr19:38503102-38503679
Coord A exon
chr19:38503680-38506315
Coord C2 exon
chr19:38506316-38507053
Length
2636 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TATCGCTGCTTCTCTTTCAGCCA
3' ss Score
8.96
Exon sequences
Seq C1 exon
GCTTGAGCGCCGCGCGCGAGCGTTTCCCTTCCCCCTGCGAGCGCCCGGATAATGTCTGAGAATGTCCATTTCTGGGACGCTTAGCAGCTATTATGTCGACTCGATCATAAGTCACGAGAGTGAGGACGCGCCTCCAGCCAAGTTTCCTTCCGGCCAGTACGCGAGCCCCCGGCAGCCGGGCCACGCGGAGCACCTGGAGTTCCCCTCGTGCAGCTTCCAGCCCAAAGCGCCGGTGTTCGGCGCATCCTGGGCGCCGCTGAGCCCGCACGCGTCCGGAAGCCTGCCGTCCGTCTACCACCCCTACATCCAGCCCCAGGGCGTCCCGCCGGCCGAGAGCAGGTACCTCCGCACCTGGCTGGAGCCGGCGCCGCGCGGCGAAGCTGCTCCGGGGCAGGGCCAGGCGGCTGTGAAGGCGGAGCCGCTGCTGGGCGCGCCTGGGGAGCTGCTCAAGCAGGGCACGCCCGAGTACAGTTTGGAAACTTCGGCGGGCAGGGAGGCCGTCCTGTCTAATCAAAGACCCGGCTACGGGGACAATAAAATTTGCGAAGGAAGCGAGGACAAAGAGAGGCCGGATCAAA
Seq A exon
GTAAGTTATAAAAAGTGAGGAAATACCCAGGCCGAAGGCCAGGCGAGGGGGAGGGGAGGGGAGAGGCAATAAACTGCGGACAATGTGAAGGGAAACCGCGGCGTTGGCCAGAGAGCAGGCGAGGGCGGAGGGAAGACGGAGGAAGGAAGGGAGGCAGCTGGGTGCCCCAGAAAGGGAGACTGAGGCCGCCGGAGGCGCGCCGCCCCACTCCGTCAAGTCCAGCGGGAACCCGGGGCTCAGGGATCAGCTCGCCGCTCTCTCGGCCTCTCTTCCCCCACACCCCGGAGGCCCGCCGAAAGCCCGGGAAGAGGCCGACAACCGCCGGCTGGGAGAAGAGCTGGCGGGGCCGGGGAGGCAGCCAGAGAAGCCGAGAGCCCGCGCGGGCCAGGGCGGGAGCGCGCCGGGAAGCCGGGCCCTGCACGGCTGGCAGGGCTCCCCGCGCCACGCGCACACCGTAAAAGCCGGCCAAGGGGAAGTGGGAGGGGGCTCATTAGGATTTTATTTGCGATGCAACAGCTTGGCGGAGGATTGTTCCTAGCAGATCTCGCTCAGTAGCCGCTCAGGGTCCGCAGCCGGCGCCGGGAGGGGCGGGGGAAGCCCAGGACCTAGAGACTGAGCCCCCTCCCGGGATGCGCCGGCCCCTCCCCAGGAGCCTTCCCTCCGGTCGCCGCCTCCCCTCCTTTGGCATTCTCGCCCGGGTTGCGGCTTCCTTTCCTGCGGTTCCCGCTGCTCTCCGCAGGGCTCCCTAGCCCCAGCCGGAGCTGTCCGCCTCGCGGGGAGTCGAGGAATCGCTTCCGAACTTCAGGGCCGACCCGCGGCGTGGAGAGAGATCCCGAAAGGACCCTGGGGAGAGGAAGGGTGGGGGGAAGAGAGGCTTGCGGAGAGGCGGAGAACTTTATCCTCGGAAGGTAGTTTCTCACCGTCTCCCACCCCTCCAAATGCACCCCCTCCAGGAACCCCAGTCTGCCTAATTTCCAGGAGGTGCTGCTCCCTAAGGGGATCAGAAAGAGTCTCGGATTTTTCGTTTTTTAAGGCTGAGAAGGGCAAGTTGGTCGGAGCTCTTAGGCCCCAAACAATAACCTGCAGGCTGGTGGGGACAAGTCCTCACCCCTTACTCTTTTTCAAGAGTGAGGGTCAGATTTTTTAAGTCTCTGCTTGCCCTGCCGGATTTCCCACCAACAGAGTGACCCACGGGTCCTTTGGGGTTTATTGCCTGCTGGAGGGAAGAGAGCTGCCCTACTCCCTCAGGTCACCCCTTCCAACCTGCCAGGTGGGATCACAAGAGCTGACATTTGGGTAACACGGCTCTTCCCAAAGCCTCCCTGCTCACACCCAAGCAGGCCCCCCACCCCAGGCCCCCAAACTCTGCCTGGAAAGTCCATTATTGCAAGGCAGCAGTTTGGCTAGGATCAATTATTAACAGTTTTTTTTTTTTTTCCTCTTTCATATTTAATGTGACTGCGGGTCTCATCCCAGGCAATCACATTAAGGAAATAGCACTGCAAATTGGTAAGACAGGGTACTTAGTGTAGGATGAACCAGATTATTATTACTTTAAAAAAAAAAAATTCAGTGTTTTTCATTTGAGATGAAGAAATCTAGCAGAGGGTGGCTGCTATTTTTAATTAACTCTGCTTTATTTGGCAACTTTTCTGAGTTCAGGGGTAAGGAGAAGAGAAACTTGCATATATTTTTGTTTCCTTTTTATCCCCCACTTCCCCTCAGTCACCCTTTTCTCTGTTCCCTCTCACCGGGTGGAGCCAGTTGGATTTAGGTGTGCTGTGATGGACTTCTGTTACCCCCACATGATCCATGGCTCCCCACCTTGGGACTGGAGCAATCTTGCGTCCCAATTTCCCTGAACTTGCTTTAACCAAACTGCGAGATGAGCAGGAGCGGAAACGGAGACTATTGCGACCATAAGTTATCTGTGAGCCCCCAGCGCTCTCTTGTCCACAGGCTGGAGGTGATAAATGGTTGTAATTGGGTTGCATGTGAATTGGAGTGTGCTGAATGTTTGCGTCTTTAAATGCAAACCATATTTGTGGTGTGTGGTGTTGGGGGGGGTGGGCAGCGAGATATCACATAGACACATATGCCTGCTGCCATGTGGCCGAGAGACCCACGCTTGTGATTAAGACAGGAGGGTGCACTGGACTGGAGGGCCAGGAGGCCCCTCAGTTTGGCTGGGCAGAAGCCACTCTCCTCTCCCCCAGCTCAGTCTTTCTCTTACCTCTCAGACTTAGAGCTAGTACTCTTCAGTCAGCCTAGTTAGTCTTGTAGAGCTGGTGGGGGAGGGGGCTTCAGCCAGGCTGGGCTCTGACCTGAATCCTAACCAGTTCTGACCCAAGCCGAGAAAGAGACTGAGAGAGGGCCTGGGACAGGGAAAGCCTGGGAAGTTGTGGGATGCCTGGCACAGGTTTGGCTCTATCCTGTCCCAAAATCTCTCACCTGGAAATGTCTATAGCAACTCCTGGCCCATCTCTGAGACCCTTTCTGGGAGCTGAAGGCCCAGGTGGCCCTTTCTCTAATGCAAAATGGGGAGTAGAGACCAAAGGGGCACCCTCTTGGAAGGAGAACACAGGGGCCCTTCACCCCCTTTCCTTTCTTTGATTCTATCGCTGCTTCTCTTTCAG
Seq C2 exon
CCAACCCCTCCGCCAACTGGCTGCACGCTCGCTCTTCCCGGAAAAAGCGCTGTCCCTACACCAAATACCAGACGCTGGAGCTAGAGAAGGAGTTTCTGTTCAATATGTACCTCACCAGGGACCGTAGGCACGAAGTGGCCAGACTCCTCAATCTGAGTGAGAGACAAGTCAAAATCTGGTTTCAGAACCGGCGGATGAAAATGAAGAAAATGAATAAGGAACAGGGCAAAGAGTAAAGATTCCTCTAGCCCACCCCACCCCTTCTCCATCTCACACTTATTTATAAGTGATGGCTGCAGAGCCAGTGCTGTCTGGGATGTATTCAAGTGAATGGGGAAGGGGATCTTTCTCTTCAAAGTCCTTTTCTGTATCTAGAGGCTCTCTCCTTTCCTTTGCCCTCACCTGTCCTTCTCTTCTCCCTGGGTCTCAGGAGGAGTTTTTATTGATTTAGAAGGTAGATGTAGTTGATTCCTAAGAAGGTGATGGGCCACAAGGAAAGACAACCCCTAGTAGAGTCCCTAGTAACCCTCCTAATTTTTCTGGGCAACCCCAGTTCCTCACTTCCAACCTGCCTGTTCCTTCCCACATACTTATCCCAAAGTCACCCGGGGACACTCCAAATGCACACAGCCCAACAGATGCCCGCCTGGATAAAGCCTGGAGCCCACAGTAACAATGGGAAAAGCCCACAGTCAACACTCAAGTGACACCCCAAGTGCCATCACACCCCACGTCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000025009:ENSBTAT00000034888:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.688 A=NA C2=0.308
Domain overlap (PFAM):
C1:
PF046178=Hox9_act=WD(100=99.4)
A:
NA
C2:
PF0004624=Homeobox=WD(100=72.2)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development