RnoINT0122882 @ rn6
Intron Retention
Gene
ENSRNOG00000032708 | RT1-Bb
Description
RT1 class II, locus Bb [Source:RGD Symbol;Acc:3469]
Coordinates
chr20:4043741-4045498:+
Coord C1 exon
chr20:4043741-4043887
Coord A exon
chr20:4043888-4045231
Coord C2 exon
chr20:4045232-4045498
Length
1344 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
CTGACGATGTCCGTCCGCAGGGG
3' ss Score
9.09
Exon sequences
Seq C1 exon
AGAGGGCACAGCTGGTGTGAGTCCTGGTGACTGCCATTACCTGTTCCTTAGAGATGGCTCTGCAGACCCCCAGCTTCCTCCTCCCGGCAGCTGTGGTTGTGCTGATGGTGCTGAGCAGCCCAGGGACTGAGGGCAGAGACTCCCCAA
Seq A exon
GTAAGTGCAGGGCAGGCTCCCCAGAGCCAGCACTCTGGGGTGGGTGACTGGTTGGTTCTGAGGGGCCCTGGGGGCCCTGGGATGTGGGGGTGGGGAATGGCAAAATTCTGATTTTGTAACAGTCTTTTACCATAGATTTCCTTTCTCTGGAGAGAGGGCGAGACTTCATTCTCATTTCTGTGTTCTAATGTAGGAGTTAGGATGGTGCTTGCCACACAGGGCGAGCCTGGCAGGTAAAAGTAGAAGGCAGAGTTTAAATCTACCACCGAAGATAAGACAGAGCATGGGGCTGTGCACAAAGAGACAACGGGGTTTACAATACCGCCCCCCTCCCGACGCCCAGCATCCTGTCTGGAGGAAAAGTCAGATTCTGAAATGCGGAAACAAGCCAGCGATAGTCTGTGGTCCTGGTGTTTGAGGAAAATTCCTGAGGTGGAGTGGAGGTTTTAGAGAGGTGAACTCTAGGTGTCTAACTCTGAGAGAAGCCAGTGGCCAAGGAGTCTGAATTTTTTGGTCAAATGGAAACGAGGACTCAGACATGGGCTTCATAAATTGAATTTCTAAGGAAACACTGGGCCTAGAAGGGAAATAAGTGACACATACTTGGGAGGTGGGGTGGGGGTCCTAGTTCTGAGACCGGAGAGTACTTTATATAAAGCCCTAGCCCTCTAAGCCGGTGCACATAGGTGGCTTCCTTCTTTCAGTTACCCTTAAGATGCCTGGAGTGACCCACACAAGCGGGCAGTTTCCAGAGGCTACCAGGATTCCCATTTGTCTGTTTTGCTCTCCTGAGAACGAGCGCCCCTATGGGCGAGGTCAGGGCCTTTTGCACACCGTAGAGGATCTCACGGGACCGGGTCAGGGTCGCAGAAACAGCCGAATATACTATTTCTCTTTCGATCGTAGTTTTATTAGTTCGTTGAGAATTTCATACAGTTTTGGTCATATTCACCTCCTCTTCCAACTCCACCCAGACCCACCCCCTTCTACCCACCTAACTTTGAGTGTTCCCTAATTTTTTTTCAAATGCACCAAGCGCGGTTTGTGTTTCCTGAGGAGTATTCTTGTGAGGACGAGCTCGGTCGCCCACTCCTTCCTTGTTCTTCCTTACCCGGGTGGAACCGGGTGAAGGCGCCCAGCTCCGGGGAAGCGGGGTCCGCACGGGCGAGTCCCGACCCCCGTCTAAGCGCGGCCTGCGGCGGCACAGGGTCTGTCGGTCCCGAGGCGCCAAGGCCGGGCGGCCCCAGAGAGCGGTCGCCCCACGCGGGAAAGCCGGCGCGGGGTGGGGCCGCCGTGGTCTCCGTGGTCCCCGCTGTACCCCGGGCTGACGATGTCCGTCCGCAG
Seq C2 exon
GGGATTTCGTATTCCAGTTCAAGGGCCTGTGCTACTACACCAACGGGACGCAGCGCATACGGCTCGTGATCAGATACATCTACAACCGGGAGGAGTACGTGCGCTTCGACAGCGACGTGGGCGAGTTCCGCGCGCTGACCGAGCTGGGGCGGCCCTCAGCCGAGTACTATAACAAACAGTACCTGGAGCGGACGCGGGCCGAGCTGGACACGGTCTGCAGACACAACTACGAGGAGACGGAGGTCCCCACCTCCCTGCGGCGGCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000032708:ENSRNOT00000000525:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.011
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0096914=MHC_II_beta=WD(100=81.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCTGGTGACTGCCATTACCT
R:
CGTAGTTGTGTCTGCAGACCG
Band lengths:
357-1701
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]