RnoALTA0018398-2/3 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000007585 | Hoxb8
Description
homeo box B8 [Source:RGD Symbol;Acc:1586211]
Coordinates
chr10:84131495-84132801:+
Coord C1 exon
chr10:84131495-84131918
Coord A exon
chr10:84132698-84132700
Coord C2 exon
chr10:84132701-84132801
Length
3 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
GTCCTTTCCCCCATTCCCAGCAG
3' ss Score
6.62
Exon sequences
Seq C1 exon
ATGAGCTCTTATTTCGTCAACTCACTGTTCTCCAAATACAAAACCGGGGAGTCCCTGCGCCCCAATTATTATGACTGCGGCTTCGCCCAGGACCTGGGCGGCCGACCCACCGTGGTGTACGGTCCCAGCAGCGGCGGCAGCTTCCAGCACCCTTCGCAAATCCAGGAGTTCTACCACGGGCCATCGTCGCTGTCCACGGCTCCCTACCAGCAGAACCCGTGCGCCGTGGCGTGCCACGGGGACCCGGGCAACTTCTACGGCTACGACCCTCTGCAGCGCCAGAGCCTGTTCGGTGCGCAGGATCCAGACCTGGTGCAGTACGCAGACTGCAAGCTCGCGGCAGCCAGCGGCCTGGGCGAGGAGGCCGAGGGGTCTGAGCAGAGCCCGTCGCCCACACAGCTCTTCCCCTGGATGCGCCCTCAAG
Seq A exon
CAG
Seq C2 exon
CCGCCGGACGCAGGCGAGGCCGCCAGACCTACAGCCGCTACCAGACCCTGGAGCTGGAGAAGGAGTTCCTATTTAATCCCTATCTGACTCGCAAGCGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007585-0-3,0-2,0-1-2/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.261 A=NA C2=0.500
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=55.3)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
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:
ACACAGCTCTTCCCCTGGATG
R:
AGGAACTCCTTCTCCAGCTCC
Band lengths:
101-104
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]