BtaALTA0014134-2/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000039581 | HOXD4
Description
Bos taurus homeobox D4 (HOXD4), mRNA. [Source:RefSeq mRNA;Acc:NM_001101087]
Coordinates
chr2:20795282-20797028:-
Coord C1 exon
chr2:20796024-20797028
Coord A exon
chr2:20795383-20795479
Coord C2 exon
chr2:20795282-20795382
Length
97 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGG
5' ss Score
10.19
3' ss Seq
CGATCTGTTTTGTCTCTCAGTGA
3' ss Score
9.11
Exon sequences
Seq C1 exon
TGGAAGAAGAAAAAAAGACAACACGAGAAAAATTAGTATTTTCTACCTTCTGAAATTAATGGCCATGAGTTCGTATATGGTGAACTCCAAGTATGTGGACCCCAAGTTTCCTCCGTGCGAGGAGTATTTGCAGGGCGGCTACCTAGGCGAGCAGGGCGCTGACTACTACGGCGGCGGCGGTAGCGCGCAGGGGACTGACTTCCAGCCCCCGGGGCTCTACCCACGGCCCGACTTCGGTGAGCAGACCTTCGGAGGCGGCGGCCCCGGGCCCGGCCCGTCTCTGCCCACGCGGGGTCACGGGCCAGAACCCGGCGGCCCCGGCGGCCACTACGGTGCTTCCGGAGAGCCATGCCCGGCTCCCTCCGCGCCCCCGCCCGCACCCCTGCCAGGCGCCCGGGCCTGTAGCCAGCCGGGAGGCCCCAAGCAGCCGCCCCCCGGGACTGCCCTCAAGCAGCCGGCAGTGGTCTACCCGTGGATGAAGAAGGTGCACGTGAATTCCG
Seq A exon
TGAACCCCAACTACACCGGCGGGGAGCCCAAGAGGTCCCGGACGGCCTACACCCGGCAGCAAGTCCTAGAACTGGAAAAAGAATTTCATTTTAACAG
Seq C2 exon
GTATCTGACGCGGCGCCGTCGGATTGAAATCGCTCACACCCTGTGTCTTTCCGAGCGCCAGATCAAGATCTGGTTCCAGAACCGGAGGATGAAGTGGAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000039581-1-1,1-0-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.764 A=NA C2=0.631
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=50.9),PF105004=SR-25=WD(100=67.9)
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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGTAGCCAGCCGGGAG
R:
CAGATCTTGATCTGGCGCTCG
Band lengths:
174-271
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development