RnoINT0116940 @ rn6
Intron Retention
Gene
ENSRNOG00000027278 | Pramef8
Description
PRAME family member 8 [Source:RGD Symbol;Acc:1564061]
Coordinates
chr5:162194286-162195621:+
Coord C1 exon
chr5:162194286-162194598
Coord A exon
chr5:162194599-162195033
Coord C2 exon
chr5:162195034-162195621
Length
435 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TCTCCCTGTTTCACTCACAGAAG
3' ss Score
10.02
Exon sequences
Seq C1 exon
GTTCCTTCAGACTGAAGATTTGAAGGATGAGTGCCCAGGACTCACCCACACTGCTGAAGCTGGCAGTACTGAGACTACTGAAGGATGAGGCCCTGGCCGTCTCTTCTCTGCAGTACTTGCCCAGGGCTCTCTTCCCACTATTGTTCAAGGAAGCCTTCAATCACAGACAAACTAATGTCCTGAGGGCCATGGTGGCAGTGTGGCCCTTTCCCTTTCTCCCTCTGGGGACCCTGATGAAGACTCCCCACCTGGAGATCTTGCAGGCTGTGCTGGATGGAGTAGACATGCTGTGGACACAGAAGGTTCTTCCCAG
Seq A exon
GTAAGGCAGACCCAGGTAGGGGGATGCTAGGGTACAGGGAAGATACATCTGGAGTAGGAGAGAGTGGGGTCAAAGGAAGATTAGAAGCTTCTGGGGGTGTCATCTTGGAAGATTATAGAAGCCTTAACCCCTTTGATCCCAGACGTATAGCACAGCTGGGTATGGAGTACAGCCGAAAGCAGCTGTGGCCCCAGTGGATAAATCTTTCCCCGGCTCTTGCAGAGGTGCTAGAGGTGAAGAGGCAGAAGTCAAGAGGAAGGGAATGGAGGAAGCAGGACAGGTCTCCAGATGCAGCCAATACTTAGAGCCCTTTCCTGGAGGCAGGAGGTGCTGTCTGGAAACCACACAAACATGCGTAAGACAGGCAGCATCAGGGACGCAGAAGACTGCTCGGTCTTTTGTATCTTCTGACACTTCTCCCTGTTTCACTCACAG
Seq C2 exon
AAGGCGGAAGCTTCAAGTGCTGGACCTGAGGAATGTGCACCATGACTTCTGGGATGTTTGGGTTGGACCAGAGGATGGAGGCCGCTCGGCAGAGGCTGTGTGTGAAGAGCAGACAGCGAAGCGCCTTCACAGATACGTACTGAGGCGGCGTTTGAAGGTGGTCACTGACCTCTGCCTCAGGTTCCACCTGAACGAGCACCAAGCATACCTGTTGCAGTGGGCCCAGCAGAGAAGAAGTTCCATTCGGCTGTGCTGTGTGAAGATGCAGATTTGGGCTTTGCCTGCGTACACCGTCCGGAAGGTCTTGATGGTGTTCCAGCCAGACAGCATCCAGGAGTTGGAACTCAATACAGGTTGGAGTCTCTCCACTCTGGTGCATTTTGCATCTTACCTGGACCAGATGAGAAACCTACAGAAGCTCCTTATAACACGGATTCACAAGAACACCTTCAAGGTACTAAATACCTCCTCGGACATACAGAAGTGTATCACCAAGTTTGTTTCTCAGTTCTCCAAACTCAACTCTCTCCAGCATCTCTCCATGAACGGCATCTACTTTTCCAGTGAGCACATGAAACAGTTGTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000027278:ENSRNOT00000037875:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.005
Domain overlap (PFAM):
C1:
NO
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:
TAATGTCCTGAGGGCCATGGT
R:
CAGGTATGCTTGGTGCTCGTT
Band lengths:
352-787
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]