RnoINT0122956 @ rn6
Intron Retention
Gene
ENSRNOG00000000777 | RT1-S3
Description
RT1 class Ib, locus S3 [Source:RGD Symbol;Acc:735037]
Coordinates
chr20:3176933-3178018:+
Coord C1 exon
chr20:3176933-3177208
Coord A exon
chr20:3177209-3177742
Coord C2 exon
chr20:3177743-3178018
Length
534 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCCC
5' ss Score
5.77
3' ss Seq
CTTACAACTCTCTCCCTCAGACC
3' ss Score
9.31
Exon sequences
Seq C1 exon
AATCTCACACGCTGCAGTGGATGTACGGCTGCGACGTGGGGCCCGATGGGCACCTGCTCCGCGGTTATTGTCAGGAGGCTTATGACGGCCGGGATTATATCTCCTTGAACGAGGACCTGCGCTCCTGGACCGCGACTGACATGGCCTCACAGGCCTCTAAGATCAAGTCAGAGGAAGTTGGTGAGGCCCATCACCAGAGGGCCTACCTGCAAGGTCCTTGCGTGGAGTGGCTCCACACATACCTACATCTGGGAAAGGAGACGCTGCTGCGCTCAG
Seq A exon
GTGCCCTGGAGACCCCTCCTTAGTTTTCCTCTGGGGTTTGGGGGGAAAGGCTTGGGGTATAGCTCAGGGGCAGAACGCTGTCCAGCAGCCACAGTGCTGAAGAGAAGGGAGAAAGACTCCCAAGGCTGCTTTTCCTCTGTAGGAAGACTAAGCCTTAATCAAGCAGATCAGCCTTGACAATGTCCCTGGACCCATTAGGGGCATTTTCTCAGGCCTCCCTCTATGCCCTACTCAGTGTCTCTAGAGTCAGACTCCAGCTTTTCTCAGTCTCTAGGCCCTCACCCAGCTCAGGACCAGAAGCCCATCCCAGGAGTCTGCAGAGACCTGGAGTCTCCTGCCCCATATTGTCACACTCACATCCTAAAGCATCACAAAGAACAGCTCCTCGCAGGTGCATGTGCTCCTGCTGGTGTCTGGAATGTGGACACCCTAATCCCATCCCAGGTCTCCTGACCATCCCAGGATGGTCACATGAACAATACTGTGTCCCTGGAAGAAAGCTAGATGCCTCATTCTTACAACTCTCTCCCTCAG
Seq C2 exon
ACCCCCCAAAGGCACATGTGACCCTTCACCCCAGACCTGAAGGTGATGTCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCTGACATCACCTTGACCTGGCAATTGAATGGGGAGGACCTGACCCAGGACATGGAGCTTGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCAGCTGTGGTAGTGCCTTCTGGGGAGGAGCTGAAGTACACATGCCATGTGGAGCATGAGGGACTGCCTGAACCTCTCGCCCTGAGATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000777:ENSRNOT00000001036:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.086 A=NA C2=0.161
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(49.2=94.6)
A:
NA
C2:
PF0765410=C1-set=WD(100=93.5)
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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCGCGGTTATTGTCAGGAG
R:
GGTCCTCCCCATTCAATTGCC
Band lengths:
343-877
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]