BtaALTD0010403-1/2 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000005546 | HOXB7
Description
Bos taurus homeobox B7 (HOXB7), mRNA. [Source:RefSeq mRNA;Acc:NM_174342]
Coordinates
chr19:38518955-38521061:+
Coord C1 exon
chr19:38518955-38519055
Coord A exon
NA
Coord C2 exon
chr19:38520805-38521061
Length
0 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACG
5' ss Score
10.52
3' ss Seq
CCCGTAAATACTCTGCGCAGGGA
3' ss Score
5.14
Exon sequences
Seq C1 exon
TCCCGGCGACTCTGCCAAGGCGGCGGGCGCCAAGGAGCAGAGGGACTCGGACTTGGCGGCCGAGAGTAACTTCCGGATCTACCCCTGGATGCGAAGCTCAG
Seq A exon
NA
Seq C2 exon
GGACCGACCGCAAGCGAGGACGCCAGACCTACACCCGCTATCAGACCCTGGAGCTGGAGAAGGAGTTTCACTACAATCGCTACCTGACGAGGCGGCGGCGCATCGAGATCGCGCACGCGCTCTGCCTCACAGAAAGACAGATCAAGATCTGGTTCCAGAACCGCCGCATGAAGTGGAAAAAAGAGAACAAGACCTCAGGCCCCGGGGCCGCCAGCCAGGACAAGGCCGAGATGGAGGAGGATGAGGAAGAGTGAGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005546-0-0,1-0-1/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.112 A=NA C2=0.369
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=67.1)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCCGAGAGTAACTTCCGGAT
R:
GGGCCTGAGGTCTTGTTCTCT
Band lengths:
246-353
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development