BtaINT0073179 @ bosTau6
Intron Retention
Gene
ENSBTAG00000009979 | HOXB2
Description
Bos taurus homeobox B2 (HOXB2), mRNA. [Source:RefSeq mRNA;Acc:NM_001191335]
Coordinates
chr19:38583393-38585653:+
Coord C1 exon
chr19:38583393-38583774
Coord A exon
chr19:38583775-38584542
Coord C2 exon
chr19:38584543-38585653
Length
768 bp
Sequences
Splice sites
5' ss Seq
CAGGTCGGT
5' ss Score
7.53
3' ss Seq
CCAGCCCGCTTTCCCCGCAGATG
3' ss Score
12.09
Exon sequences
Seq C1 exon
ATGAATTTTGAATTTGAGAGGGAGATTGGGTTTATAAACAGCCAGCCATCGCTCGCCGAGTGTCTGACTTCCTTCCCCGCTGTCTTGGAGACATTTCAAACTTCATCAATCAAGGAGTCGACATTAATTCCTCCTCCTCCTCCTTTCGAGCAAACCTTCCCCAGCCTCCAGCCCGGCGCCTCCACCCTTCAGAGACCCGGGAGCCAAAAGCGAGCCGAAGATGGGCCCGCTCTGCCGCCGCTGCCGCCGCTCCCCGCCGCCCCCCTGGCCCCCGAGTTCCCCTGGATGAAAGAGAAGAAATCCGCCAAGAAACCCAGCCAATCCGCCGCGTCTCCCCCGGCCGCCTCCTCCGTCCTGGCCTCCGGGGTCGGATCGCCGGCAG
Seq A exon
GTCGGTAAGCGTGATAGGGGTTGGGTGAGGGGCAGCTAGAAAAAAAGGGGGAGAAAGAGCGATGGGGGAGGTAGAAAAAGGTGTCGAGCCTGTTGGGGTTTCTTGCCCCCGTCGATTCCAGGGACGAGAAAGCAGAAAAGATCGTTTTGGTTCAGGCCTGGCCGCTGCCAGCATTTTGGTTTTTTCCCTTTCCCTACAGCAGATTTTGGAAGCCGATTGGGGAAGAGCATCTTTTTCTGCTAGGAGAAAAGGATTCGATTGAGGTTTCACATTTAGCTGTGTGGAGGAGTATTGTTGGATGGGGTCGAATCTGGAGGCAGGAAAAGATTCTATCCCATCTAATCTAGCTCTAGGAGAAGAGGGGGAATTTGAGAGCTGGGGGCTAGGGAGGAGAAGAGGTGAGGAACAATCTTTCTTTATGAATCCTCTCCCCAGGCTGAGTTGGAAAGTGCTGAAATGAGGGATCCACTCGGAGGACCTGGGAGGGGCTCTGAGGTTCTGGGGGCGAAGGGGAGCCGCTCCGTAACCCCTGCATGGTCCGTGGGCGGCTCTCTGAATGCTGCGCGCTGACTCTGGCCGGGTCTGGCGGAGAGAGAGAGGGACGAGAAAGAAGGCAAGAGCCGTGGGAGCGAGCCGCTTTGGTAGGCGGGCAGGTTGGGGGTGCCGCTGACATTGTTTTGGGAGGATGGGATAGTCTTTTATTTCAGCCGAGTTGAGGTTGGGCTGAGGACACGGCCCGCGTTGACGCCCAGCCCGCTTTCCCCGCAG
Seq C2 exon
ATGGGCCGGGACTGCCGGAGGCCGCCGGCGGCGGGGCGCGCAGGCTGCGCACCGCTTACACCAATACGCAGCTGCTGGAGCTGGAGAAGGAATTCCACTTTAACAAGTACCTGTGCCGGCCGCGCCGCGTGGAGATCGCGGCCTTGTTGGACCTCACCGAGAGGCAGGTTAAAGTGTGGTTCCAGAACCGGCGCATGAAGCACAAGCGGCAGACGCAGCACCGAGAGCCGCCCGACGGGGAGCCAGCCTGCCCGGGCGCGCTGCGGAACACCGGCGAGCCAGCCGAAGAGCCTGTGGCTAGCCCGGGTCGCCCCTCCGTATTGCAGGCCTCGCGAGCAGCCTGTTGTCTCACGCCCGAGGTCGCGCAAGGGCCTCCGGGCGTCTCGGGCCCCCGGGCTTTGGCCGCTCGCGTGGAGGGCGCAGACGCGCGGAGCCCGGGCGGCGCGCTGCGCGGGGCCGGCGGACGGGAGCCGGAGCCGTTGCCAGAAGACGCCTTCTCAGAGCGGCAGGATTCGCCTTTCTTGCCGGACCTCAGCTTCTTCGCGGCCGATTCCTGTCTCCAGCTGTCCGGAGGCCTCTCCCCTAGTCTCCAGGGCTCTCTGGACAGCCCGGTTCCCTTTTCCGAGGAAGAGCTGGACTTCTTCACCAGCACGCTGTGTGCCATCGACCTGCAGTTCCCTTAATAACCCGCTTCCTTCTCTCGACCCCCGGCCCCCCTCAGCAGCCTGCGGGGAAACCCAAGGACCCCCCTCCCCAAGTTGTATGGACTTCTTTATGTGTTTTGCTAAAATTCAGGTATTATTGAATTAGCGTTTAATCCACCTCCTTTCTTCTCTAAAATATTGGACACACGGGCGTCTTTTACAAATTACACATAAAAAAATCCGTTTGGTAGAGTCCTTCCAACGAAATCTCAGGAATAATTAAACTCTGGGGAGCGGGGGTGTGCTTTCTTAAGAACTAGAGGAACCTATTTTCCTCTCTGTCTCTTTTTTTTTTTTTAAGTTTTAGGCCGTAGATTATTTATTAAAATTCTTTACTAATAGGAAAAGGGGAAAGTATTTATTGTACATTATTTTCATAGATTAAATAAATGTCTTTATAATACGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009979:ENSBTAT00000013159:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.695 A=NA C2=0.573
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=25.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCCTCCTCCTCCTTTCGAG
R:
ATTCCTTCTCCAGCTCCAGCA
Band lengths:
346-1114
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development