RnoINT0122883 @ rn6
Intron Retention
Gene
ENSRNOG00000032708 | RT1-Bb
Description
RT1 class II, locus Bb [Source:RGD Symbol;Acc:3469]
Coordinates
chr20:4045232-4047125:+
Coord C1 exon
chr20:4045232-4045498
Coord A exon
chr20:4045499-4046843
Coord C2 exon
chr20:4046844-4047125
Length
1345 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
GGGATTTCGTATTCCAGTTCAAGGGCCTGTGCTACTACACCAACGGGACGCAGCGCATACGGCTCGTGATCAGATACATCTACAACCGGGAGGAGTACGTGCGCTTCGACAGCGACGTGGGCGAGTTCCGCGCGCTGACCGAGCTGGGGCGGCCCTCAGCCGAGTACTATAACAAACAGTACCTGGAGCGGACGCGGGCCGAGCTGGACACGGTCTGCAGACACAACTACGAGGAGACGGAGGTCCCCACCTCCCTGCGGCGGCTTG
Seq A exon
GTGAGCGCTGCGGGTCCCGCGGGAGCGCGGCGGGCTGTGGGGGGTCGTGGGGGAACACGGAGCAGAGTTCCGGCGTGAGGAGCTGCCGTGGCTTCCTTCCTCCGGTCAGTCCCACAGCACAGAGCGAGCGCCCCCTTGGAGTCTCCCTCCTTCCTCACCTTTGCCCTGTGCGGCCCAGCTCCCCTCTGACCCCTGGCTCTGCTGTGGCAAGACCGGGAGCTCCACGGCTGGCGGCCTGTGGAAGCGGGTTAACCGTTATGTCGGGTGGTTATCCCCGCCATTCTGTTGCCCCATTCCCCTTGTCCCTTTGAGGGCTGTTTGCTGCCTGGCGCTGACCTGAAGGCGTCACCGCCATTTTCCTCCTTCTCTGAGGTAAACTGTGTTGACTTGGATCACACTAAAAGTTTGTGATACAAAATCCGAGGGACTCCTTTCTGTTTCCACTCCCGGATACCCCCAGAGCCTTACACATGACACCAGCGTCATGTTAGGCATCGCGTTCAGATTTAATGTCCTACATGACTAACGGTTAACTCGAAAGGTTAAGCTTGCTTTCCTCATGGTCTTGTTTGGCAACTGATTCCTCACAGCACCGGAATGCAGTGATGGCCGCCAGGAATTAATGCACTCGGCTGTGGGGAAAAACAGTCAGAGAGAGTAGAAGATGAGAGACCAAAACATGCTCTCAGTTCATTAAATACGTGAAGTGTGTATGCTGTTTCCAATTGAAGGGATAACAGCACCCGGCAAGGAGCTTTTGAGGTAGTGGGCACAATATGTCAAAGCCAGTCGGGAAACACATCTGTCCAGCTGCACATGACAGTCTGAGGAGACGAAGGAAGGATGTCGTACTACAGTCATTTTCCCAATTTTTTCCTCAAAATTATTGACTTGAACTCAGAATCAGTTTTTCTTTTGTCTTATCTGTTTGTTTTAGAAAAAGTTTATTTTTATATTTTTGCATAAATAAAATTTATTTTATGTAAATAAAATATACTTCATTTTATTTACCCATAAATTTAAAAAATACATAGAGGGTTTACAAAGAGGGTTTCTTGTGTGCTTCTGGCTGTCCTAGAACTTGTTGTAGGCCAGGTTGGCCTCATAGAGATCCCCCTGTCTCTACCTCCTGAGTGCATCACCGCCCGGCTTCTTTTGTTTCCCTACATTTCATATTATAGAAGGACAGGGCCGCACCGACTGTTTTCCTAGTGAGTTAAATCTGTATTGTGGGGTTGATCTTTATCCACTGTTAGGACCTGGCATTCATTCCCACCCTGCCTCTTCTCTGTGGGGAGTCTCCACACGGCCCTCATCTCACTCACTGTCTTTTCTGTCACCCTAG
Seq C2 exon
AGCAGCCCAATGTGGCCATCTCCCTGTCCAGGACAGAGGCCCTCAACCACCACAACTTGCTGGTCTGCTCAGTGACAGATTTCTACCCAGCCCAGATCAAAGTGCGCTGGTTCCGGAATGGCCAGGAGGAGACGGCGGGGGTCGTGTCCACACAGCTTATTAGGAACGGGGACTGGACCTTCCAGATCCTGGTCATGCTGGAGATGACGCCTCAGCGGGGAGAGGTGTACATCTGCCATGTTGACCACCCCAGCCTCGAGAGCCCCGTCACAGTGGAGTGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000032708:ENSRNOT00000000525:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.011 A=NA C2=0.008
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
Mouse
(mm9)
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:
358-1703
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]