DreALTA0013938-2/2 @ danRer10
Alternative 3'ss
Gene
ENSDARG00000056027 | hoxb8a
Description
homeobox B8a [Source:ZFIN;Acc:ZDB-GENE-990415-108]
Coordinates
chr3:23557361-23559020:+
Coord C1 exon
chr3:23557361-23558163
Coord A exon
chr3:23558917-23558919
Coord C2 exon
chr3:23558920-23559020
Length
3 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
CTAAACTTCTTTATTGCCAGTAG
3' ss Score
3.32
Exon sequences
Seq C1 exon
GCTACTGCGCTTATATAAAGACATTCTATCGTAATCTCTTGAACAAAATCAGTACCACCACCAACAGCAGTAAAAGATGAGCTCATATTTCGTCAACTCTCTCTTCACTAAGTACAAAAGTGGAGACACTTTACGACCAAACTATTACGAGTGCGGATTTGCTCAGGACCTAGGGACGAGACCCACCGTCGTGTATGGTCCAGGCACCGGGGCCACTTTCCAGCATGCTCCTCAAATTCAGGAGTTTTACCACCACGGCGCATCCACGCTCTCCGCTGCGCCTTACCAGCAGAGTCCATGTGCGGTAACCTGTCACGGCGAGCCGGGTAACTTCTACGGTTATGATGCTCTCCAGAGGCAAACACTTTTCGGTGCTCAAGACGCCGACTTGGTTCAGTATAGCGACTGCAAGCTCGCCACGGGGGGCATCGGCGACGAGACGGACAACACAGAACAGAGTCCGTCGCCCACACAACTGTTCCCGTGGATGCGACCTCAAG
Seq A exon
TAG
Seq C2 exon
CTGCCGGACGGAGACGAGGCCGTCAGACCTACAGCCGCTATCAGACGCTCGAACTGGAGAAAGAGTTTCTCTTCAATCCCTACCTAACACGCAAGCGTCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000056027-0-2,0-1-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.197 A=NA C2=0.519
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=54.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACACAACTGTTCCCGTGGAT
R:
TCTCCAGTTCGAGCGTCTGAT
Band lengths:
92-95
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]