RnoALTD0024681-5/6 @ 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
chr20:4045499-4045870
Coord C2 exon
chr20:4046844-4047093
Length
372 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAC
5' ss Score
7.2
3' ss Seq
TGTCTTTTCTGTCACCCTAGAGC
3' ss Score
8.98
Exon sequences
Seq C1 exon
TTCAAGGGCCTGTGCTACTACACCAACGGGACGCAGCGCATACGGCTCGTGATCAGATACATCTACAACCGGGAGGAGTACGTGCGCTTCGACAGCGACGTGGGCGAGTTCCGCGCGCTGACCGAGCTGGGGCGGCCCTCAGCCGAGTACTATAACAAACAGTACCTGGAGCGGACGCGGGCCGAGCTGGACACGGTCTGCAGACACAACTACGAGGAGACGGAGGTCCCCACCTCCCTGCGGCGGCTTG
Seq A exon
GTGAGCGCTGCGGGTCCCGCGGGAGCGCGGCGGGCTGTGGGGGGTCGTGGGGGAACACGGAGCAGAGTTCCGGCGTGAGGAGCTGCCGTGGCTTCCTTCCTCCGGTCAGTCCCACAGCACAGAGCGAGCGCCCCCTTGGAGTCTCCCTCCTTCCTCACCTTTGCCCTGTGCGGCCCAGCTCCCCTCTGACCCCTGGCTCTGCTGTGGCAAGACCGGGAGCTCCACGGCTGGCGGCCTGTGGAAGCGGGTTAACCGTTATGTCGGGTGGTTATCCCCGCCATTCTGTTGCCCCATTCCCCTTGTCCCTTTGAGGGCTGTTTGCTGCCTGGCGCTGACCTGAAGGCGTCACCGCCATTTTCCTCCTTCTCTGAG
Seq C2 exon
AGCAGCCCAATGTGGCCATCTCCCTGTCCAGGACAGAGGCCCTCAACCACCACAACTTGCTGGTCTGCTCAGTGACAGATTTCTACCCAGCCCAGATCAAAGTGCGCTGGTTCCGGAATGGCCAGGAGGAGACGGCGGGGGTCGTGTCCACACAGCTTATTAGGAACGGGGACTGGACCTTCCAGATCCTGGTCATGCTGGAGATGACGCCTCAGCGGGGAGAGGTGTACATCTGCCATGTTGACCACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000032708-2-12,3-12,4-12,5-12,7-12,8-12-5/6
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
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 Inclusion Isoform:
NA
Other Inclusion 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:
GGCCTGTGCTACTACACCAAC
R:
GGAACCAGCGCACTTTGATCT
Band lengths:
358-730
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]