BtaEX0017356 @ bosTau6
Exon Skipping
Gene
ENSBTAG00000003304 | HOXC4
Description
Bos taurus homeobox C4 (HOXC4), mRNA. [Source:RefSeq mRNA;Acc:NM_001102373]
Coordinates
chr5:26136686-26138815:-
Coord C1 exon
chr5:26138335-26138815
Coord A exon
chr5:26138175-26138223
Coord C2 exon
chr5:26136686-26137850
Length
49 bp
Sequences
Splice sites
3' ss Seq
CCTTCCCCCTCTCTCTCCAGGAG
3' ss Score
13.7
5' ss Seq
TGGGTAATT
5' ss Score
6.19
Exon sequences
Seq C1 exon
AAACGACAAAGCGAGAAAAATTATTTTCCACTCCAGAAATTAATGATCATGAGCTCGTATTTGATGGACTCTAACTACATCGATCCGAAATTTCCTCCATGCGAAGAATATTCGCAAAATAGCTACATCCCTGAACACAGTCCGGAATATTACGGCCGGACCAGGGAATCGGGATTCCAGCATCACCACCAGGAGCTGTACCCACCACCGCCTCCGCGCCCTAGCTACCCTGAGCGCCAGTATAGCTGCACCAGTCTCCAGGGGCCGGGCAATTCGCGAGGCCACGGGCCGGCCCAGGCGGGCCACCACCACCCCGAGAAATCACAGCCGCTCTGCGAGCCGGCGCCTCTCTCAGGCGCCTCCGCCTCCCCGTCCCCAGCCCCGCCAGCCTGCAGCCAGCCAGCCCCTGACCATCCCTCCAGCGCCGCCAGCAAGCAACCCATAGTCTACCCATGGATGAAAAAAATCCACGTTAGCACGG
Seq A exon
GAGCGACTCTGGGTTAGCACAATTGAACTGGATTTACGAGCGAGAATGG
Seq C2 exon
TGAACCCCAATTATAACGGAGGGGAACCCAAGCGCTCGAGGACAGCCTACACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCATTACAATCGCTACCTGACCCGAAGGAGAAGGATCGAGATCGCCCACTCGCTGTGCCTCTCTGAGAGGCAGATCAAAATCTGGTTCCAAAACCGTCGCATGAAATGGAAGAAGGACCACCGACTTCCCAACACCAAAGTCAGGTCAGCGCCCCCGGCCGGCGCTGCGCCCAGCACCCTCTCCGCAGCCACCCCGGGCACTTCTGAAGACCACTCCCAGAGCGCCACGCCGCCGGAGCAGCAACGGGCAGAGGACATTACCAGGTTATAAAACATAACTCACACCCTGCCCCTATCCCAGGCCCCCCATCCTCCCCTCACACACAAATTGACTCTTATTTATAGAATTTAATATATATATATATTTTGGTTCTTTTCTCTCTTCCTCCCACCTTCCCCCTTGTCAGTTCCAAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003304_MULTIEX1-2/2=1-C2
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence inclusion (Alt. Stop)
No structure available
Features
Disorder rate (Iupred):
C1=0.796 A=1.000 C2=0.669
Domain overlap (PFAM):
C1:
NO
A:
NO
C2:
PF0004624=Homeobox=WD(100=47.9)
Main Inclusion Isoform:
ENSBTAT00000004277fB3292
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCAGCAAGCAACCCATAGTC
R:
CTCTAATTCCAGGACTTGCTGCC
Band lengths:
132-181
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development