BtaINT0073177 @ bosTau6
Intron Retention
Gene
ENSBTAG00000007603 | HOXB1
Description
Bos taurus homeobox B1 (HOXB1), mRNA. [Source:RefSeq mRNA;Acc:NM_001205954]
Coordinates
chr19:38594902-38596261:+
Coord C1 exon
chr19:38594902-38595481
Coord A exon
chr19:38595482-38595932
Coord C2 exon
chr19:38595933-38596261
Length
451 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
TTCTCTTGCCCCGCCCCTAGCGA
3' ss Score
8.07
Exon sequences
Seq C1 exon
ATGGACTATAATAGGATGAACTCCTTCTTAGAGTACCCACTCTGTAACCGGGGACCCAGCGCCTACAGCGCCCACAGCGCCCCTACCTCCTTCCCCTCGAGCTCGGCTTCTGCTGTTGACAGCTATGCAGGCGAGACCCGCTATGGTGGGGGGCTGCCCAGCTCTGCACTGCAGCAGAACTCAGGCTATCTGGCCCAACAGCCACCCTCGGCATTAGGGGTGCCCTTCCCCAGCTCTGCGACCTCGGGGTACTCCCCGGCTGCCTGCAGTGCCAGCTACGGGTCTTCTCAGTACTACCCTCTGGGCCAGCTGGAAGGAGATGGAGGCTATTTTCATCCTTCAAGTTACGGGGCCCAGCTAGGGGCCTTGTCCTCCGATGGCTATGGAACCGCTGGAGTGGGCCCAGGGCCCTACCCTCCACCACAGCCCCATTATGGGAACGAGCAGACAGGGAGCTTTGCACCGGCCTGTGCTGATCTCCTCTCCGAGGACAAGGAATCGGCCTGCACGTCAGAAACGAGCACCCCTACAGCCCAGACCTTCGACTGGATGAAGGTTAAGAGGAACCCACCCAAGACAG
Seq A exon
GTAGGGCTCAGATGTGGCCACCCCCTCTCTAGGGGCTCAGAGCGGCTCTGCTGCTTTTGCACTGAGGTGTCCTGGGCTGGGTTCCTGTCTGCACCACCGGGTAGAGGCAGGTAAGAGCACTGTGCTCAGTCTCAGGTCAGGTGGGGTCTCCCCACCCAGTGAGTGCCCAGTTATCCTTAAGAGTAAGTCTCCAGACACACCCCTACTTCGATCTGTGTGCTCAGCGCAGGCCTAGGACCTGGTGTTCCGAGGAGGGGGAGCTCGGGGGTGGAAGTGTGGGGCCTGCTCCAGGTTGCCTGGAGGGGTGCCTGGTGATCCATGGAAACTTTGAGAGCTGAAGCTGGATAGAATGGTGACTGGGGGTGCAGAGCTGGCGGGGCAGGGGGGCGGTGGGGAGGGGAAGGAGAAAGAGGAGAGAACTGACGTGGCCCTTCTCTTGCCCCGCCCCTAG
Seq C2 exon
CGAAGGTGTCCGAGCTGGGCCTGGGCGCGCCAGGTGGCCTCCGCACCAACTTCACCACTCGGCAGCTGACCGAACTGGAGAAGGAGTTTCATTTCAACAAGTACCTGAGCCGGGCCCGGAGGGTGGAGATCGCTGCCACCCTGGAGCTCAATGAGACGCAGGTCAAGATATGGTTCCAGAACCGGCGCATGAAGCAGAAGAAGCGGGAGCGGGAGGGAGGCCGGGTGCCCCCAGCCCCTCCAGGCTGTCCCAAGGAGGCGACTGGAGACACCTCCGACCAGTCCACGTGCACCTCCCCAGAAGCTTCGCCCAGCTCTGTCACCTCCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007603:ENSBTAT00000009997:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.412 A=NA C2=0.706
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=50.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGGAAGGAGATGGAGGCTA
R:
CTTCTCCAGTTCGGTCAGCTG
Band lengths:
355-806
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development