RnoINT0004980 @ rn6
Intron Retention
Gene
ENSRNOG00000061639 | AABR07044404.1
Description
NA
Coordinates
chr20:4676802-4677506:-
Coord C1 exon
chr20:4677260-4677506
Coord A exon
chr20:4677078-4677259
Coord C2 exon
chr20:4676802-4677077
Length
182 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
CTGACCGCGGGGTCCCGCAGGCT
3' ss Score
5.61
Exon sequences
Seq C1 exon
GTCACCGCGGTGTCCCGGCCCGGCCTCGGGGAGCCACGGTTCATCTCTGTCGGCTACGTGGACGATACGGAGTTCGTGCACTACGACAGCGACGAGGAGAATCCGAGGATGGAGCCGCGGACGCGGTGGGTGGAGCGGGAGGGGCCAGAGTATTGGGAGGAGGAGACGCAGAGAGCCAAGAGAAGGGAGCAGTGGTACCAAGGGAGCCTGAGGAACCTGCGCAGCTACTACAACCAGAGCGAGGACG
Seq A exon
GTGAGTGACCCCGGGTCGGAGGTCACGACCCCTCCGCGTCCCCACACGGCCAGAGAGGTCCCTGGTCCCAAGTCCGAGGTTCAGGAGAAGAACAGACACGGGCCGGTTTCCCTTTCAGTTTTGAGGAGTCCGCGGGCGGGCGGGGCCGGGGTGGGGCGGGGTCTGACCGCGGGGTCCCGCAG
Seq C2 exon
GCTCACACACCTTCCAGAAGATGTATGGCTGTGACGTGGGGTCGGACGGGAGCCTCCTCCGCGGGTATGTGCAGTTCGCCTACGATGGCCGCGATTACATCGCTCTGAACGAAGACCTGAAAACGTGGATGGCAGCGGACACGGCGGCACAGATGACCCGGAGCAAGTGGGATCAGGCTGCTGAGGCAGAGAGAAAGAGGGCCTACCTGGAGGGCGAGTGTGTGGAGGGGCTCCGCAGATACCTGGAGCTCGGGAAGGAGACGCTGCTGCGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000061639:ENSRNOT00000061297:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.313 A=NA C2=0.097
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(48.0=98.8)
A:
NA
C2:
PF0012913=MHC_I=PD(51.5=94.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGGTTCATCTCTGTCGGCTA
R:
CCCACGTCACAGCCATACATC
Band lengths:
252-434
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]