RnoALTA0018403-2/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000042480 | Hoxd8
Description
homeobox D8 [Source:RGD Symbol;Acc:6489440]
Coordinates
chr3:61627864-61628436:+
Coord C1 exon
chr3:61627864-61627942
Coord A exon
chr3:61628333-61628335
Coord C2 exon
chr3:61628336-61628436
Length
3 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGG
5' ss Score
5.87
3' ss Seq
TGTTGTTGTTTTTTAATCAGCAG
3' ss Score
5.13
Exon sequences
Seq C1 exon
AATATTGGCGGGACCCCAGACCCCTTAAATCAGAGCTCGTCTCGCTTCTCAAATCGTTTCCCTGAGATGAGACCACAAG
Seq A exon
CAG
Seq C2 exon
CTCCTGGTAGACGGAGAGGAAGACAAACCTACAGTCGCTTCCAAACCTTAGAGTTGGAAAAGGAATTCCTTTTTAACCCTTATCTGACCAGGAAGAGAAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000042480-4-5,4-4-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.510
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=57.6)
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:
ATCAGAGCTCGTCTCGCTTCT
R:
GGTTTGGAAGCGACTGTAGGT
Band lengths:
98-101
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]