RnoALTD0021430-2/2 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000010736 | Pbx4
Description
PBX homeobox 4 [Source:RGD Symbol;Acc:1305100]
Coordinates
chr16:21308824-21310650:-
Coord C1 exon
chr16:21310561-21310650
Coord A exon
chr16:21310460-21310560
Coord C2 exon
chr16:21308824-21308959
Length
101 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGG
5' ss Score
7.2
3' ss Seq
CTGAGCATCTCTGTCTGTAGGCG
3' ss Score
7.17
Exon sequences
Seq C1 exon
GCCTGTCGTGAGTTCACCACGCACGTCACCAACCTTCTCCGGGAACAGAGTAGGGTGAGGCCCGTGTCCTCCGGGGAGATCGAGCACATG
Seq A exon
GTGAGCACCATTCACAGCAAGTTCAGTGCCATCCAGAGGCAGCTGAAACAGAGCACCTGTGAGGCTGTGATGACCCTACGCTCACGGTTCCTGGATGCCAG
Seq C2 exon
GCGCAAGCGGCGGAATTTCAGCAAGCAAGCCACCGAGGTGCTGAATGAATACTTCTATTCCCATCTGAGCAACCCTTACCCCAGTGAAGAGACCAAGGAAGAGCTGGCCAGGAAGGGTGGCATCACAGTGTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010736-8-9,9-9-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.188 A=NA C2=0.239
Domain overlap (PFAM):
C1:
PF037928=PBC=PD(31.1=95.3),PF070286=DUF1319=PD(64.7=85.9),PF083976=IMD=FE(51.2=100),PF0004624=Homeobox=PU(0.1=0.0)
A:
NA
C2:
PF083976=IMD=PD(26.8=71.7),PF0004624=Homeobox=PU(75.0=97.8)
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTGTCGTGAGTTCACCAC
R:
CTGGGACACTGTGATGCCAC
Band lengths:
226-327
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]