RnoALTD0021192-3/3 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000015642 | Pabpc4
Description
poly(A) binding protein, cytoplasmic 4 [Source:RGD Symbol;Acc:1305015]
Coordinates
chr5:140979536-140983366:+
Coord C1 exon
chr5:140979536-140980146
Coord A exon
chr5:140980147-140980450
Coord C2 exon
chr5:140983173-140983366
Length
304 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TGAGTGTTCCTCCTTGACAGCTG
3' ss Score
8.86
Exon sequences
Seq C1 exon
GTCCCGCCTCGGAGCCTCCCTGCTCCAGCCTCTCCCAGCGTCGCTGGTGCCACCTGTGCGCTGCGGCGCGTGCCACAGCTCTTCGGAGCCCCTTTTGTCCTGCAGTAGGCCCTGCAAGAAGTCCTGGCGGGGCTCGGGGTAGTAGGGGGTGGGGAGATGAACGCTGCGGCCAGCAGCTACCCCATGGCCTCCTTATACGTGGGCGATCTGCACTCCGATGTCACCGAAGCCATGCTGTATGAAAAGTTCAGCCCTGCGGGGCCTGTGCTGTCCATCCGGGTCTGCCGCGATATGATCACCCGCCGCTCTCTGGGTTATGCCTACGTCAACTTCCAGCAGCCAGCTGACGGTGAGTAGGAGCGGTGTGCACACATTCGGGAGATTCCTGGGGACCTTGGGAGTGCTGTAGGCGGAGGCCAAACTGCCAGGGCTGGGGAACATACTAAATAGCATGTAGCCAGAGAAGCCTGGATGGAAGCACGAGGCAGAGGTTGAGCCAG
Seq A exon
GCATGTGGTCACGACCCCGGCTTCAGTCTTCCACCACTTGGTAACCTGATGACCTTGGGCTACTGGGTGGGGGTGGGGTAGAGCAGGGATTGGAACCCAAGGAGATTGGAAATCGGGATCCGAATAAAGTGACTTGGCTATTCTAGTGTATATATAACCCCCTTCAAGTAGAAGTGGATCTGTTGTAGACCCTGGCATGAATTGGCACTCCTCAATGGATTGAAACAACACCCTCAAAAGTATAGGTTTCAAGACTGCTGGCCCTAACCTAGACTGACGATTTGAGATGGCTTTAGGAAGCAAG
Seq C2 exon
CTGAGAGGGCCTTGGACACCATGAACTTTGATGTGATTAAGGGGAAGCCAATCCGGATCATGTGGTCTCAGAGGGACCCCTCTTTGAGGAAGTCTGGTGTGGGAAATGTCTTCATCAAGAACCTGGACAAGTCTATAGACAACAAGGCACTGTATGACACTTTCTCTGCCTTCGGAAACATCCTGTCCTGTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015642-2-2,3-2,4-2-3/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0007617=RRM_1=PD(25.4=27.7),PF0007617=RRM_1=PU(40.6=43.1)
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:
CGATCTGCACTCCGATGTCAC
R:
ATCCGGATTGGCTTCCCCTTA
Band lengths:
355-659
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]