RnoINT0122938 @ rn6
Intron Retention
Gene
ENSRNOG00000060412 | RT1-M4
Description
RT1 class Ib, locus M4 [Source:RGD Symbol;Acc:1562593]
Coordinates
chr20:2044525-2047226:+
Coord C1 exon
chr20:2044525-2044803
Coord A exon
chr20:2044804-2046950
Coord C2 exon
chr20:2046951-2047226
Length
2147 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
TTCTCCTCTGATCTCCTCAGATC
3' ss Score
10.27
Exon sequences
Seq C1 exon
AGTCTCACACTGTCCAGTGGCTATTCGGCTGTGACATAGGGCCAGACCGTCGCCTCCTCCGTGGGTATAAGCACGTTGCTTATGAAGGCCAGGATTACATCTCTCTAACTGAGGACCTGCGCTCCTGGGTTGCGGTGGATACCGAGGAGGCTCAGATCACCAGGCGCAAGTGGGAGGCATCTGGTATTGCTACATCATGGAGGTCTTTCTTGGAGGGCAGGTGCGTGAAGTGGCTTCTCAAATACCTGGATAAAGGGAAGGAGATGCTGCAGCGTGCAG
Seq A exon
GTATGAGGGGTAGCTTCTATTGACCCTTGAGCAGAGTTTATGGAAAGGAAAGAGAATGGGACCAATTCCTAAGCCACCTGTTGTGAAATACTGTCCCCCCCCCTCCACCCCCCACCCTGCCAGGCTGATAATGTTTCAAAATCAGAATAGCTGTGATTACCCTCACTGGGGATTCAGGATGGTGTGTGTGTGTGTGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGAATTGATGAAGTCCGTTGGTGGCACACTCTAGTACGGTAGCTTTTGTGAGCTGTCATTCATACTGGATGGGCTTTTCGGTGTTGTAGTCGTTTATGAGTACTAAGTAGCTCCTCACTCGTGCCTGTAAGTAACCTTCAATAAATGTATTGATGGACTTGGATGGAAATCCTTCATTTGGTCTGTGGTTGAAGTCCTTTCTGGGCTGGATAGATATCTATCATCACTCTCCAGAGAAAGCAATAAGCCGCTTTACACCTCAGACCAAACCACTCTACACAGCAGGGCCAAAATGGGCTAGGGAGGATCAGTTTCATGGTTCCCACTATGGGATGTAAAATGTGAAATTGAAGGCAAACCATCCACGGTGGGAATTACTCGTGTGGCTCTGCTTTTCTCTGTGTGGTGTGGAATGGCGGCTGAGGGTTGCACTGGCATGGGGGACAGGGCTCACATCCGGGACTGCTCCATCCTAAGGCGTATGGATACCTATGCCGGGAATACCAGGGTGGTTGTCTTCCTCCGCGTGGCATGAGATCTGTCACGACACTGACAGCAATTTCTGAAACAACCCCTGTGGGGCAGGATTCTAAGCAGACAGTGGCAGCACTTATGTGGCCTTCCCTATGGACGGTTGAGACTTGCAACTAGGGCTGAGCCATCTTCCCAGAAAGACCTTGCCCACCTAAGGGAGGAATTACAATGGGAAGAAGGTGTGCAAGTGCTCCCCCCCCCCTTTTTTTCTTTTCTAACTTCAAATTGGAGTGAAAATCGGAAAGGGGGAACGTCAGAATTGAGGTGCTGGCTTACCACTTGTTATGGCTGGGTTGGTGGTGGTGAAGGAAGGCATAAGGGAAAGAGTAGAAATTAGATCTGTGCTCCCGGAATCCAAAAGCTTGGAAACTGTGGTAAGAATAAAACAATAAAGAAAAAGAAAGTGAAGTAAAAGTAATTGGATACCCCCCCACCCCCACCCCCCCGCACAGGCCAAGCTTTAGTTCAGAGAAAACCTTATGATTCAGCATGCATTTGAGGCCTTAACTAATGACTCAGTGTGGGAAATCTTGATAATCAGGAGTCTTCTGACTCTGAGCCCCCCCCCCCCCCAGCTGGGGACCGAACCCAGGGCCTTGCACTTGCTAGGCAAGCGCTCTACCACTGAGCTAAATCCCCAATCCCACCTCTGAACTTCTTGAAACAAAAGTTTAAAGGAAAATTAAACAGCCCCTACAAAGGGCTCTCATGGCCGTGGGGCATAGATGCAGATGGGATCTGAGTGATGTAGAAGTGGAGAAATTGAGTGCTGTCACTGCTCATTCCTGTGCAGTCTAAGGCAAAACGAAAGAATCATTGGGTCAGCAAGACGTTTGGTGCTCGCCATAGAGCCTGACAACCTGAGCCTGGAACCCTGAGCACACATGGCAGAAGGAGAGAACAGTTGTCTTTTGACCTTCAGATATGTGCTACACATGTATAGGTACACACACACACACACACACACACACACACACACATACACACACACACACAGGATCTCCCAGTAACCAACTCTCTTCAGCTACCGCATCCTAAATATTCCACTAGAGTCATCACCATCACCAGATACAAAGCATCAAACACCTGACCCATGGGGGGAACATTTTACATTCAAAGCACGGTAGTGACTCCATCTTTTCTGGGATGAAGGGGCACCAACTCTGAAGAGTGGGTGCCAGTTCCACTTTGATCTCACCCCGTTTCTGCCAATGTTCACAGATCAGGAATAGTTCCAAGGAATAGGTATTTCTACCTCCTAAGTCCATGCTGTTTTAAGAGATGCTTTCTAAATTTTCAACCCAACTACGGGGATGATCACATGACCAATGCTCAAATGGTTCACAGGAAAAAACAAGTTGTTCTCCTCTGATCTCCTCAG
Seq C2 exon
ATCCCCCCAAAACAAACGTGGCTCATCACCCTAGACCTGAAGGTGATGTCACCCTGAGGTGCTGGGCCTTGGACTTCTACCCTGCTGACATCATCCTGACTTGGCAAAGGGATGAGGAGGACCTGACCCAGGACATGGACCTTGTAGAGACCAGACCTACAGGGAATGGAACTTTCCAGAAGTGGGCATCTGTGGTGGTGCCTTCAGGAGAAGAGCATAGATACACATGCCATGTGCTGCATGAGGGGCTGCTTGAGCCCCTCATCCTGAGATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000060412:ENSRNOT00000030174:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.203
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(49.7=94.7)
A:
NA
C2:
PF0765410=C1-set=WD(100=90.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]