RnoINT0122928 @ rn6
Intron Retention
Gene
ENSRNOG00000049590 | RT1-M2
Description
RT1 class Ib, locus M2 [Source:RGD Symbol;Acc:3493]
Coordinates
chr20:1337503-1338738:-
Coord C1 exon
chr20:1338463-1338738
Coord A exon
chr20:1337779-1338462
Coord C2 exon
chr20:1337503-1337778
Length
684 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAA
5' ss Score
7.09
3' ss Seq
TTCCAACTCTTCTTCCTCAGATC
3' ss Score
9.51
Exon sequences
Seq C1 exon
GTTCTCACACCATCCAAAGGATGACTGGCTGCTACATTGGACCAGACGGACACCTACTTCACGCATACCGTCAGTTTGGATATGATGGACAAGATTACCTCACTTTGAATGAAGATCTGAGCACCTGGACTGCGGCAGATTCGGCAGCTGAGATCACCCATAGAGAGTGGAAGGCAACTAATGAAGCTGAGTTCTGGAGGGTCTACTTGGAGGGCCCTTGCATGGTGTGGCTCTTTAAATACCTGACAGTGGGAAATGAGACTCTACTGCGCGCAG
Seq A exon
GTACAAGGGGTAAAAAAGTAACTCCTCCTGATGAACTGGAGCTCATCAGGAATTTCAGATGGTCTCATCAGAAGGGAGAAAAAATGATACCATCTGGAATTCTCTGTATGTCTGTCCTTTGTCTCTGTGTCTCTGTCTATCACTCACAATCTCTGTGTCTATCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCACACACACACACACACACACACACACACACACACACCAGGAGAGGGAAGAATGGTCCTGGGATTTTTGGTCCAATATCGGTTCAGAATTTATCTCAAAATAGGAGAAAAGATCCCTAAAGTTGCCATTCCCTTCACAGCTGCAGCCCATGGCCTCTCTCAGGTTATTTTCTCTGGCCACACTCAATGGTATGGCACAGTTGCAGTGATGTAGAGTTTCTTGGCCTCACTCAGTCAGGACAAGATTTTTATTTTTCCTGGTAACCCAGCATCTCCTACCGTAGGCCAGTTCACCTTGATTCTACAACTTTTCAAGCAATCTATTATTGCAGATGCCTGAGTACAGTTGCTGTGTAGGTCTGGGCATATTCCCCTGACTATTTCCAAAATAATTACAAGAATAACACCGAGTCCCAAGAAAAAATGTAAATGTGCAAAATTTCCAACTCTTCTTCCTCAG
Seq C2 exon
ATCCCCCCAAAGTATATGTGACCCATCACCCCAGACCTGAAGGTGATATCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTTCTGACATCACCCTGATCTGGCAAAGAGATGGAGAGGACCTGACCCAGGACATGGACGTAATTGAGACCAGACCTGCAGGGGATGGAACCTTCCAGAAGTGGGCAGCTGTGGTGGTGCCTTCGGGGAAGGAGCAGAATTATACATGCTATGTAGAACATGAGGGGCTGCCTGAACCCCTCACCCTGAGATGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000049590:ENSRNOT00000041074:3
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=0.043
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(49.2=94.6)
A:
NA
C2:
PF0765410=C1-set=WD(100=88.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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:
CTGGAGGGTCTACTTGGAGGG
R:
ATCTCAGGGTGAGGGGTTCAG
Band lengths:
356-1040
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]