RnoINT0122939 @ rn6
Intron Retention
Gene
ENSRNOG00000060412 | RT1-M4
Description
RT1 class Ib, locus M4 [Source:RGD Symbol;Acc:1562593]
Coordinates
chr20:2046951-2047470:+
Coord C1 exon
chr20:2046951-2047226
Coord A exon
chr20:2047227-2047339
Coord C2 exon
chr20:2047340-2047470
Length
113 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAAA
5' ss Score
2.56
3' ss Seq
CTCTACCCTCTCTCTCCCAGAGC
3' ss Score
9.73
Exon sequences
Seq C1 exon
ATCCCCCCAAAACAAACGTGGCTCATCACCCTAGACCTGAAGGTGATGTCACCCTGAGGTGCTGGGCCTTGGACTTCTACCCTGCTGACATCATCCTGACTTGGCAAAGGGATGAGGAGGACCTGACCCAGGACATGGACCTTGTAGAGACCAGACCTACAGGGAATGGAACTTTCCAGAAGTGGGCATCTGTGGTGGTGCCTTCAGGAGAAGAGCATAGATACACATGCCATGTGCTGCATGAGGGGCTGCTTGAGCCCCTCATCCTGAGATGGG
Seq A exon
GTAAAAGGGTGTATGTGTGGGCACACAGTCTGTCCCTGGGGAAAGCAGGAGCCCTTCTGCAGAACTTGAGCATGTCCTTCACTTCTATCCTCCCTCTACCCTCTCTCTCCCAG
Seq C2 exon
AGCCTTCACCCTCCCCCACCACTCCCATCATGGGGATCATTGCTGGTCTGGTTCTCCTTGGAGTTTTGGTCACTGGAACTGTGGCTGCCATTATGAGGAGGAGGAAGAGTGCAGGTAAGGATGGTGTTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000060412:ENSRNOT00000030174:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.203 A=NA C2=0.047
Domain overlap (PFAM):
C1:
PF0765410=C1-set=WD(100=90.3)
A:
NA
C2:
NO
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:
ACCCTGCTGACATCATCCTGA
R:
AACCAGACCAGCAATGATCCC
Band lengths:
251-364
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]