RnoALTA0021326-2/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000047706 | LOC103690108
Description
class I histocompatibility antigen, Non-RT1.A alpha-1 chain-like [Source:RGD Symbol;Acc:9113230]
Coordinates
chr20:3791344-3791825:-
Coord C1 exon
chr20:3791622-3791825
Coord A exon
chr20:3791445-3791459
Coord C2 exon
chr20:3791344-3791444
Length
15 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
CCTTCCTTGAACTCTCACAGCTT
3' ss Score
6.5
Exon sequences
Seq C1 exon
ACCCTGAGTTGGTCAGGGCTGAGAGCTGGGGTCATGACCCCCACCTTCATTTCCTGTACCTGTCCTTCCCAGAGCCTTCTCCATCGACCGACTCCAACATGGAAACCTATGTCATTTATGTCATCCTTGGAGCTGTGGCCATCATTGCAGCTGTGATCATTGTAGCTGTGGTGGCTGTTGTGATGAAGAGGAGGAGAAACACAG
Seq A exon
CTTTTCTTCTCACAG
Seq C2 exon
GTGGAAAAGTAGGAGTCTACGCCCCTGCTCCAAGTAAGTGTGGGGAGCAGGAGTGTCCCTGAGGGTATTGGGGTGAAGCTAGAGATGTTGGGAGCTCAGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000047706-6-5,6-4-2/2
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=0.000 A=NA C2=0.154
Domain overlap (PFAM):
C1:
PF0765410=C1-set=PD(4.7=4.3),PF066236=MHC_I_C=PU(13.3=2.9)
A:
NA
C2:
PF066236=MHC_I_C=FE(80.0=100)
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:
CTTGGAGCTGTGGCCATCATT
R:
CAGGGGCGTAGACTCCTACTT
Band lengths:
106-121
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]