RnoINT0117092 @ rn6
Intron Retention
Gene
ENSRNOG00000023679 | Prdm5
Description
PR/SET domain 5 [Source:RGD Symbol;Acc:1588700]
Coordinates
chr4:96734670-96736502:+
Coord C1 exon
chr4:96734670-96734844
Coord A exon
chr4:96734845-96736380
Coord C2 exon
chr4:96736381-96736502
Length
1536 bp
Sequences
Splice sites
5' ss Seq
ACAGTGCGT
5' ss Score
5.66
3' ss Seq
TGCCCCCTTGCTTCTTATAGTTT
3' ss Score
8.02
Exon sequences
Seq C1 exon
GTCACCTTGGCTGTGAAGAGGACTTTGCCTGCCCACAGTGTGAATCGAGCTTTCCCAGTGAGGAAGTTCTTACTGAGCACCTTCAGAGCTTGCACCAGAAGCCCACAGGGGAGAAAGAGTTCAAATGCGAGAACTGCGGGAAGAAGTTCCCTGTGAGGCAGGCCTTGCAGAGACA
Seq A exon
GTGCGTATGCTCAGTGGGGTTCCGCTTATGAATGAGCAGTCAGATTGTTCACTGTGTTTAGTATGTGTGTCTGTGTTTGTGAGCGTGTACCAATGCATGTGTGGGGAAGTGGAGGTTAGCCCACTTGGCTATGAATTAACTCATCTGAGTGTATAATGCCGAGTTTCGAATGCTCTGATCATAAGGTTTATAGGTAAACACCATTTCTGCTAAGCCCTTCTAGATGTGTTTCAAACTTGCCATTAAATATTATGCTTAGTGGTTTACTAATCTGAAATTTACATATGCATAATTTAGACAGTGCCTAAAGTTATTCATCAAGTCTCACTCATTTGCTCTCTAATTTGTTTTAAAACTGTTTGACTGATGACGAATTCAGTGTAGCAATAATGGAGGGATGGAAAGCACCATCTGTTCACAGTGAGTTGGGAGAAGAGTTTGACGGTGAATGGGTCAGAGTGTGGCAGTGAGGTGGATTACATGAATTTATCCTTTGCCTTATTATCCCAATGATTTGTGTTTACAACATAAAATTAGCTTCTCTTTTAACATCTTGTGAGGTCAGAGTTACCGAACGTGAGAGACTACAGAGACTCTAAACTTCCAGTCTAAGCAGACTGTCACCTTACGTGACTAAAACATCGGCCAGGCTTACTGTATTAATGCTTCCACTTTGTTGTGTTTAATTTCCAAGTACGCCATTTCATACCCCCTCAACCATCCATTGTCTGTCTGTCCATCTGTCTGTCTATCTATCCATATTTATCATCCATCCACCTATCTATCTGCCTGCCTACCTATCTACCTATCATGTATCTGTCATCTGCACATGTGATGTTTCTATATGTTATATGCATCAGGTTTTGCTTATGAAATCTGAAAGTAATTTTACTCACAAGCAAAAAGTCTTTGAAAAACTGATACCTTTAGGATTCCTTAAAGAGTTAAAGATTATATTAAGTTCTTCAAATCAAGCCAAGTGACAGTTATAATAAATCTTAATAAGTTAATTTCAGTTTGTATTTTAGTCAGCTTTTATATGTATTTATTGCACTGTCAGATTTTGAGCTCTGTCTTAGAGCTAAATAGGGTACCATTAAGAATGTAGAAGACCACAGCAAGGCTGCAGGAGGACGGGAGCATGTCCTGGCAGGCTCGCTTCTTCCCCTGCCCTTCTCGGTGTTCTTTCCTGCGCAGCCAGAAGCAACCTGCAGGATTCTCCACCGAGAGTTCAGTGTTCTCTTTGCAATTCTCTTTTCAGTTCAGCACTGAGCTTTAGTGTCTAGCTACGAAATGGCTCTCACTAGTCTGCAGGTCATTTTTGAGTGCATAATTCATACTTGGAGTAAGTCAGCACTATACTAAGTAATCTGAAGGATTTAGATGAGTCTTTCTTACCGACATAACTATGCATGAAATGCCCTCCATACCCCTGCAGGAAGGATGTCCTAGGATGCATGAGTGGCAGAAGCCTTTGCAGTGTTCGAGTGTGTAGGTATGCCTTCATCATGTCTTCTGCCCCCTTGCTTCTTATAG
Seq C2 exon
TTTTGAGCAGCACCAGAAGGCTTGCCGAGGGGATGCCAGGTTTGTGTGCAAGGTCGACAGCTGTGGGAAGAGGCTGAAAAGCAAGGATGCCCTGAAAAGGCACCGGGAAAATGTCCACACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023679:ENSRNOT00000009569:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.136 A=NA C2=0.167
Domain overlap (PFAM):
C1:
PF134651=zf-H2C2_2=WD(100=49.2)
A:
NA
C2:
PF0009621=zf-C2H2=WD(100=61.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCACCTTGGCTGTGAAGAGGA
R:
AGTGTGGACATTTTCCCGGTG
Band lengths:
295-1831
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]