RnoALTA0018397-2/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000008313 | Hoxb3
Description
homeo box B3 [Source:RGD Symbol;Acc:1310780]
Coordinates
chr10:84193043-84194569:+
Coord C1 exon
chr10:84193043-84193639
Coord A exon
chr10:84194466-84194468
Coord C2 exon
chr10:84194469-84194569
Length
3 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCA
5' ss Score
7.88
3' ss Seq
CCCCTCCCCCTCGGGTCCAGCAG
3' ss Score
6.11
Exon sequences
Seq C1 exon
AGGGTATCAGGCCCTTGCAAGTTGCCACCCACTGCCCGGGCCTCGCCCAGCGATGCAGAAAGCCACCTACTACGACAACACCGCAGCTGCGCTCTTCGGAGGCTACTCCTCGTACCCTGGCAGCAATGGTTTCGGCTACGACGGGCCTCCCCAGCCCCCCTTTCAGGCCGCTACACACCTGGAGGGTGACTACCAGCGCTCAGCGTGTTCCCTGCAGTCCCTGGGCAATGCCGCCCCACATGCCAAGAGCAAGGAGCTCAACGGCAGCTGCATGAGGCCAGGCCTGGCCCCAGAGCCCCTGCCCGCACCGCCGGGTTCACCCCCACCCAGCGCCGCACCTACCAGTACCACTAGCAACAGCAATAACGGGGGTGGGCCCAGCAAAAGCGGCCCCCCCAAGTGCGGTGCCAGCTCCAACTCCACCCTCACCAAACAGATATTCCCCTGGATGAAAGAGTCAAGGCAAACGTCCAAGCTGAAAAACAGCTCCCCGGGCACAG
Seq A exon
CAG
Seq C2 exon
AAGGTTGTGGTGGCGGCGGCGGCGGCGGTGGCGGCGGCGGTAGTAGCAGCGGCGGGGGCGGCAGCGGCGGCGGGGGAGGGGACAAGAGCCCCCCGGGGTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008313-6-7,6-6-2/2
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=0.840 A=NA C2=0.853
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=20.4),PF132931=DUF4074=WD(100=23.2)
Main Inclusion 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:
AGGCAAACGTCCAAGCTGAAA
R:
CCCGCCGCTGCTACTACC
Band lengths:
96-99
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]