RnoALTA0032588-2/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000042905 | RT1-T24-4
Description
RT1 class I, locus T24, gene 4 [Source:RGD Symbol;Acc:1598233]
Coordinates
chr20:3189473-3193932:+
Coord C1 exon
chr20:3189473-3189591
Coord A exon
chr20:3193666-3193747
Coord C2 exon
chr20:3193748-3193932
Length
82 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGT
5' ss Score
8.4
3' ss Seq
TCTGCACTATTCTTACTCAGCCG
3' ss Score
3.92
Exon sequences
Seq C1 exon
GCGATTTCTCTAGTTTTTCTCAGGACATAGAAGACTTAAAACAACCCTGACACCATGCTCTGACACTATGTGGGCTCTGATCTTCTGCTTCCTGAGTCACCCCCGAGACACTGGAGCCC
Seq A exon
CCGTGACAGAGCCGGGCCCAGGAGTTCCTGCATTTTTTGCCAGTGGCTTTGTAGATAACCAGCCCTTCATCCACTATGACAG
Seq C2 exon
TAGGAAGATGGAGGCAGAGCCTTGTGCTGACTGGCTGAGGGAAAATCCATATTACTTTGATGAGGAGACCCAGGTTTTCACCAATCGGATGAAGATCTTCCAGTTGAGCCTGAGAAACATTCAGCAATACTACAACAGCTCTGGTGACCGGAGTCAGAGAGCAGATGGCTTCCACCAGCAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000042905-0-4,0-3-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(0.1=0.0)
A:
NA
C2:
NA
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
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:
AACAACCCTGACACCATGCTC
R:
CCGATTGGTGAAAACCTGGGT
Band lengths:
168-250
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]