BtaINT0073182 @ bosTau6
Intron Retention
Gene
ENSBTAG00000045835 | HOXB5
Description
homeobox B5 [Source:HGNC Symbol;Acc:HGNC:5116]
Coordinates
chr19:38534840-38536253:+
Coord C1 exon
chr19:38534840-38535401
Coord A exon
chr19:38535402-38536062
Coord C2 exon
chr19:38536063-38536253
Length
661 bp
Sequences
Splice sites
5' ss Seq
ATGGTAATT
5' ss Score
6.49
3' ss Seq
CTCTGCTCTGTCTGCTCCAGACA
3' ss Score
9.78
Exon sequences
Seq C1 exon
ATGAGCTCGTACTTTGTAAACTCCTTCTCGGGGCGTTATCCAAATGGCCCGGACTATCAGTTGCTAAATTATGGCAGTGGCAGCTCTCTGAGCGGCTCTTACAGGGATCCCGCTGCCATGCACACCGGCTCTTACGGCTACAATTACAATGGGATGGACCTCAGCGTCAACCGCTCCTCGGCCTCCTCCAGCCACTTTGGGGCGGTGGGCGAGAGCTCGCGCGCCTTCCCTGCGCCCGCCCAGGAGCCCCGCTTCAGGCAAGCGGCGTCGAGCTGCTCCCTGTCCTCGCCCGAGTCCTTGCCCTGCACCAACGGCGACAGCCACGGCGCCAAGCCCTCTGCTTCGTCCCCCTCCGACCAGGCGACCCCGGCCAGCTCCAGCGCCAATTTCACCGAAATAGACGAGGCCAGCGCGTCCTCGGAGCCTGAGGAAGCGGCGAGCCAGCTAAGCAGCCCAAGCCTAGCTCGGGCGCAGCCAGAGCCCATGGCCACCTCCACAGCCGCGCCCGAGGGGCAGACTCCGCAGATATTCCCCTGGATGAGGAAGCTTCACATCAGCCATG
Seq A exon
GTAATTCTCGCTCTCGCTCCCCTTTTTGTCTTCTCGGCTTTTCCTTCTCCACGTTTGTGGGTGGGGGGAGTCGGCGAGGAGAGCTTGGCTTTTCCTCAAATATAGATTTCTCTTTTTCGGAGGGGGAGAAAAAGCTCGGAGGGACAGAGCCAAAAGAGGGCTTAGCTGGGGGGTTGAAGAGGAGTATTTTTAATAATTTGTTCACAGATTCGCCTTAGGTTTTATTTGCCCAGCTGTACTAGCTTTAGGATGAAGGATGGGGTTTATGTAACATGGGGAAGGGTCCTGCTTGCCCCCGAAATTTTGAGACTGCTTTTAGCAGAGGAGGGGCGAGCAGTAAAACGAGCTTTCCAGGGCAAAAGTGCAACCGTTCTCCTCCCTCCCGGGGTGAGCGGCCGCCTGAGCCCAGCGAAGGGTGAGGCACAGGGAGGGAGCAAGAGACAAAGCCGGGCGCATTCGCTGCGGGCAGAAGTGGGGGCTGTAGGAGAAGGGGGCATCAGGAAACAGGCTCGGATGCGGGCATCTGGAGTGGGGAGGATCGGAGCTCCTGTGAGCTGGGTGCCGGGGACGCCTGGGTCCTGCTCCACGCCCCCCTCCCACCCAGTGCCCCCTCCCTTAACCAGAATAACGCGGCCTCGCCGCTCTGCTCTGTCTGCTCCAG
Seq C2 exon
ACATGACCGGGCCGGACGGGAAAAGGGCCCGAACCGCGTACACCCGCTACCAGACCCTGGAGCTGGAAAAGGAGCTCCACTTCAACCGCTACCTGACGCGGCGGTGGCGCATCGAGATCGCCCACGCGCTCTGCCTGTCCGAGCGCCAGATCAAGATCTGGTTCCAGAACCGGCGCATGAAGTGGAAGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000045835:ENSBTAT00000065146:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.691 A=NA C2=0.234
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=89.1)
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:
CAGCGCCAATTTCACCGAAAT
R:
CAGATCTTGATCTGGCGCTCG
Band lengths:
345-1006
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]