BtaINT0073181 @ bosTau6
Intron Retention
Gene
ENSBTAG00000039599 | HOXB4
Description
Bos taurus homeobox B4 (HOXB4), mRNA. [Source:RefSeq mRNA;Acc:NM_001078114]
Coordinates
chr19:38561274-38563604:-
Coord C1 exon
chr19:38563586-38563604
Coord A exon
chr19:38562767-38563585
Coord C2 exon
chr19:38561274-38562766
Length
819 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
CTCTCTCTGTGTGTGTCCAGTCA
3' ss Score
8.13
Exon sequences
Seq C1 exon
AAAGTTCACGTGAGCACGG
Seq A exon
GTGAGTGCGTGGGCACCCCTTCCCCCTCCCACCCCCGGCGCTTTACACCAAAGGGACCTCAAGGCATGGGGGTGGGGGGAGCTAGGGGAAGCCAATTGTCCCCGCTATAAACTCGCCATTGCCGGAGATTTACGGTCGCCTGTTTTCAGAGCCACATAATTACATCCCCCATAAATTTTTATGGCCTGGTGGGCCCCGCGCCTTTGAAGTAGGTTCCCCATCCTCTGCCATTCTCACCAGCGACTTTTTCGCCAGGGAGATGCAGTCTCAGTGAAGTTGGAAATTGGGGAGGGGTGTGAGAGGTGGGGGAGGAGAAGGGGGAGGAGGTAATCTGTATTTAAGCGGAGAGTTGAGTCAACTCCCAGTATTTATTTTTTCCTTTCTTTCCTCTAGTCTGGCTTCTTGGCTAGTGGGCAAAAGTTTTTACTGGGGGCAGCACTACTTGGAATCGGAACATTGAGGGTTGGAACTAACAGAAAGGTTTAGGGAAGCCCCCTCCCTCTTTCACCCTTCATTCTCCCCATCTCGGGCCCCAGGCCAAGTAAGGGGAGAGATGAGCGATTAAAACCTTGTGAAGATTCCTCACTCCTCCCCGCCCCCTCCCCAAACAACAACGTCGTGACCGCACAGTCGTCCAAAACTTAGAGGTCTCTTTCTCCTCCTGGGGTCCCGCTTTCTCCTTCGTCCCCACCCCCTCTGGAGGAAGAAGAGGTGGCGGGAGAGGGAGGGAGACATTGCGTTAGCTGGAGGAAAGGGCTCCCCTCCTCCCTTTCGGGGCAATAAAACTTTCTCTTTCTCCCTCTCTCTGTGTGTGTCCAG
Seq C2 exon
TCAACCCCAATTACGCCGGCGGGGAGCCCAAGCGCTCTCGGACCGCCTACACTCGCCAGCAGGTCTTGGAGCTGGAGAAGGAATTTCACTACAACCGCTACCTGACACGGCGCCGGAGGGTGGAGATCGCCCACGCGCTCTGCCTCTCCGAGCGCCAGATCAAGATTTGGTTCCAGAACCGGCGCATGAAGTGGAAAAAAGACCACAAGTTGCCCAACACCAAGATCCGCTCGGGCGGCACCGCAGGCTCAGCCGGAGGGCCCCCTGGCCGGCCCAACGGAGGCCCCCCTGCGCTCTAGAGCCCCCCTTGCGGGAGCCGCGAACCTCGGGGCGGGGGTGGGTTGCGAGCTCGCGGGTGGTTGGGGGAGACGAGGGAGGGGACCCTGGGGCATGGGCCCGAAAAAGCCTACCTGCCCTCCCCCCACTTTGTCTATTTACACGAATAAATGCGGAGGAGGGGGGAGGGGAAGCTTTATTTATAGAAATGACAATAGGGAGCCGGGTGAGGCCCCCCAGAAGCAAGGTTCAAGTCTCTTGCTTTCTTCCTTAAAAAAAAAAAAAAAAAGAAGAAGAAGGAAGAAAGAAAAAGACAGAAAGAGAAATAGGAGGAGGCTGCACTCCTCATTTTCAGCTTTGGCGAAGATGGATCCACGTTTCATCTTTAATCACGCCAGGCCCAGGCCCATCTGTCTTGTTTACTCTGCCGAGGAGAGGACGGGCCTCGGTGGCGACCATTACCTCGACACCCGGCTAACAAATGAGGCCCGGCTCGGCCGCCGCCGCCTCTGCTGCTGCCGCTCTTGGAAGACAGTCTGGATTTTCTTTCTTTGTCCCTCATTCCTGAAACCCAGCGAAAGCATCCTCTGACTGCCAGATAGCACAGTGTTTTGGCCACGGTAACAAACACGCGCACACAACCTCCTTCCCCCTCCATGCCCGTTCACCCCCCTTCCACCTTGGGGCCGGGGTAGGGACGACAGGCTGGGGACAGGTGGACGTAGGGTGCCTTGGCTGCGCAGGAGCAGGGCAGGGTAATTGAGTCCGAGAGAAAAAGATGACCCAGAGACCGGGAGGGCCCTCCTTTGGAAGGTCAAGCCATGCCTGGCGGGGTGAGAGGCCAGTTGCCTTCTGGGAGCTGGACACAACCCTCTCCCCAATCTAGAGTTGTGCAGTGGAGGCCTTTTCTCCTAGATTGAAAGTGAATGTGAAACTAGGCAATAAAATGCCCTTCCCATCTGGGAGATAAGGTTACAGAGACCTCTCCCATAGTTTATCATTGTTGCATTGATGATGATGATGATTATTATTAATTATTATTATTATTATTTTATGTCATGTGCGTCTGTCCTCTCTCCTATTCTCTTTCTGACATTCCAAACCAGGCCCCTTCCTAGTCCTGGGGCTGCTTGAGTCTAGAACCCTTCGTTGGTGTGAAAATGTGTGTCATGTACAGAGTGACAATAGAAATAAATGTTTGGTTTCTTGTGATCAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000039599:ENSBTAT00000043402:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.286 A=NA C2=0.586
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=57.0)
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