RnoINT0116931 @ rn6
Intron Retention
Gene
ENSRNOG00000042820 | Pramef17
Description
PRAME family member 17 [Source:RGD Symbol;Acc:1587447]
Coordinates
chr5:162441550-162442968:-
Coord C1 exon
chr5:162442682-162442968
Coord A exon
chr5:162442117-162442681
Coord C2 exon
chr5:162441550-162442116
Length
565 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
ATCTCCTATTTTATCTATAGGAT
3' ss Score
10.28
Exon sequences
Seq C1 exon
ATGGACCTGAAAGCCCCACCCACACTCCTGCAGCTGGCTGCACAGAGCACGGTAAAGAAGGAGGTGCTGACCATCTCTGTTCTGGAGTACCTACCAAGGGAGCTCTTCCCAACGCTGTTCAAGGAGGCCGACACTCAGAGAAAAGCAAAGATGATTAAGATCCTGGTGGAATACTGGCCCTACCCTTGCCTTCTTGTTAGGTTGCTGATAGATAAACCCAACTTGGAGATCTTCCAGGCTATACTGGATGGAGTTGGCACATGGCTGAAACGGAAATATCGCCCCAG
Seq A exon
GTAAGCCAAATACCAGGTAGGGAAATCTGGGCTTAGAAGAATAAGGTAAAATGTAGATCAGAGGCTTTGGCTGGTATCTTAGAGGCCTGTAGGGGCCTGGAAAACTTCTAAGTCCTTATAACAAATTAAATATGAGATACAGGTTGATGGAGATGTCACTGCGTCTCCACCAGGTAATAGAAATAGGAGCTGACTTGCTGGGAGGTGGTGGCACACACCTTTAAACTTGGAAGGCAGAGGGAGGTGAGTCTCTGAATTTGAGGCCAGCCTAGTCCATAAAGCTACAGAGGGAGGGCTACAGAGAGAAATCCTGTCTTAAAAACTAAGAAACTTAAAAACTGGCAGAAATCTGAGGCAACTGAGCAGAGAGAAACAGGACTGGTCCCCAGATATGGCTCAGGCAAAGTGCCCTTGCTTGGCAAGCTAGAGGTTGTATTGGAGACCCAGCACTGAAAACCATGAGTATACAGAAGACAGCAGAATGGGAGACAAATTGCATCAGAAATGATGAAAAAAGTGTTAGGTATCAATTTTCCTTCTGACCCATCTCCTATTTTATCTATAG
Seq C2 exon
GATGGGGAAGCTTGAAGTGGTTGATTTGAGGAATGGACACCTTGACTCCTGGGATTTGCAGGCTGGAAGAGAGGGTGGAGGAGCCCAATCAGAAACTGTGCCTGAGAAGCAAGTAATGGAGGGCCACTCAAACAGGCGGCGTTTGAGGGTGTTCTGTGACCTTTCCTTTAAGTCTTCTAAGCATGAAGATAAACACCAAACACATCTGTTGCGGTGGGCAAAGGACAGAGAGGATTTCCTGCATCTGTGCTGTAAGAAGTTAGAGATTGGAGCATTAGAAGTGTCCAAGGTCAAGAAGGAGTTAAAATTTTTACAGCCAGAGTTCATCAAGGAGTTGGAACTGAATACAGTGGGGAATCTGTCCAAATTGGCAAAACTTGTACCTTGCATCAGCAAGATGAGAAATCTTCACAAACTCATGCTAGTACGCATCTTTGAAAGGACCTATACACCCTCAGAGAAAAACGTCTCCAAGATCATTTCTCTGTTCCCTGAACTCAGGTATCTCCAGAATCTCACTATTGGTGATGTCTATTTTCTTAAAGACCACATGAATGAGTTACTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000042820:ENSRNOT00000048366:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.084
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
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:
GTGGAATACTGGCCCTACCCT
R:
ATCCTCTCTGTCCTTTGCCCA
Band lengths:
357-922
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]