RnoALTD0024681-1/6 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000032708 | RT1-Bb
Description
RT1 class II, locus Bb [Source:RGD Symbol;Acc:3469]
Coordinates
chr20:4045249-4047093:+
Coord C1 exon
chr20:4045249-4045498
Coord A exon
NA
Coord C2 exon
chr20:4046844-4047093
Length
0 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGC
5' ss Score
7.43
3' ss Seq
TGTCTTTTCTGTCACCCTAGAGC
3' ss Score
8.98
Exon sequences
Seq C1 exon
TTCAAGGGCCTGTGCTACTACACCAACGGGACGCAGCGCATACGGCTCGTGATCAGATACATCTACAACCGGGAGGAGTACGTGCGCTTCGACAGCGACGTGGGCGAGTTCCGCGCGCTGACCGAGCTGGGGCGGCCCTCAGCCGAGTACTATAACAAACAGTACCTGGAGCGGACGCGGGCCGAGCTGGACACGGTCTGCAGACACAACTACGAGGAGACGGAGGTCCCCACCTCCCTGCGGCGGCTTG
Seq A exon
NA
Seq C2 exon
AGCAGCCCAATGTGGCCATCTCCCTGTCCAGGACAGAGGCCCTCAACCACCACAACTTGCTGGTCTGCTCAGTGACAGATTTCTACCCAGCCCAGATCAAAGTGCGCTGGTTCCGGAATGGCCAGGAGGAGACGGCGGGGGTCGTGTCCACACAGCTTATTAGGAACGGGGACTGGACCTTCCAGATCCTGGTCATGCTGGAGATGACGCCTCAGCGGGGAGAGGTGTACATCTGCCATGTTGACCACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000032708-2-12,3-12,4-12,5-12,7-12,8-12-1/6
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.011 A=NA C2=0.003
Domain overlap (PFAM):
C1:
PF0096914=MHC_II_beta=WD(100=81.1)
A:
NA
C2:
PF0765410=C1-set=WD(100=87.4)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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:
CAACTACGAGGAGACGGAGGT
R:
CGTCATCTCCAGCATGACCAG
Band lengths:
253-357
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]