RnoINT0117091 @ rn6
Intron Retention
Gene
ENSRNOG00000023679 | Prdm5
Description
PR/SET domain 5 [Source:RGD Symbol;Acc:1588700]
Coordinates
chr4:96732982-96734844:+
Coord C1 exon
chr4:96732982-96733156
Coord A exon
chr4:96733157-96734669
Coord C2 exon
chr4:96734670-96734844
Length
1513 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTG
5' ss Score
8.56
3' ss Seq
GTGTTGTACATTGCACACAGGTC
3' ss Score
6.87
Exon sequences
Seq C1 exon
GAAGGAGAAAATATTTTCTACTTGGCAGTCGATGATATAGAAACAGATACAGAGCTTTTGATTGGCTACCTGGACAGTGATGTGGAGGCAGAGGAGGAGGAGCAGCAAGCTCTGACCATGGCCAGAGAAGGCAAAGTTGACCACTCTAAGGGACAGTTGGCAGCTGGAAGTAAAG
Seq A exon
GTACTGCATCTTCGTTCGGTGATCTGAAGGAGGAAACATTGAAGAGGAATGTAGCCTGCATTATTTGAATTATACTTGTGTGTTATTATCTGGTATTATTAAAACAGATTTTGTCAAAACTATTCATCATCTCTGAATAGCAGAAAAAGATCGTGTAAGTACCAGGTATGTCCTGTAGAGTGACCAAGGTAAGAGGGGCAGCTCTGGTTCTTTTCACTGTGATAGCATAGAGAGAAGGGCTGTCTCTTCCTGCACTGGCTCTGCCAGCGTCCAGTAAGAAGCTCACTCAGGCTCTGAGGGTTTCATCCCATGTACATGTGAGGAGGGCAGATCTGTAGGGTGGTCCTGCTGTGTCCTGGAGATCTGTCTTCTGAGATCTTCAGAGAATCTGGACATTCTGGAAATCTATTTTTAGTCTAGTAAAAGGAGTGGATAAGATTGCTAAATTGTCCTCATCTGTGGATCAAAAACTTCAGGTGACCATAGGTGATACCTGAAGTCTAGGAGATAGATGCCAATTCATTGTCAACTGATACGAAATAATCCTTTATTATTGGTTCTGTTTTATTCCTGCAGAAAATGTGAGGGAAAGTGTTGTGTTGTAGCACATGGTATCTTTGTCAATTTGGATGAAACAATACTTTTAAACAGTCAGAAATTTCTCGTTCACAGTTCTGTCTGCAGTTTACACTCAAGCCGAGGGACCAGCACAAGTCTGACTTCTTTCTCATTTACAAGAGTTAAACCTACAAGACACAAACATGACCGCAGCAAAAGAAACAAAGATGTCAGTCACATGTTTACCAGTGTAGCATTTGATTATATGAATGTGGCACCTTAAATATGTAAATGACTTAGAGTTAGAAGTAAGAAAAAGAGCACCATGGGACAGTGTGCCTAAGGTTTGATCACAGACAATGCACTCACAGACCAGACACATGTGGCTTTGGTATGGACAACTGTGTCTTCAGGGTGGCATTATTAGTGATTTTAATTTTTTCATATTTAATATATTTTAACACAATGGCCTTCTGAAGGACGTGGGTGAAGCTCTGCCAGGGGCGCCTCACTCCTGTACCTGCACAGACAGCACCTTTTTCAGGCTGTACCTTATTTCACATCGGTGTGAGATCCCCCTTTGGCAATTGACGATAGTGTATGTCTGTTGGATTCTTCTCCTTGTAAAGTTCAGAGTGAACTAGAGATGATTTCAGGAAAAAATTTGCTTTGCAGTTCAACAAACAAATGCAGTTGTCATTTGTTATCTAAAACATTACCATTAAAAGGGAAATTACAGATTGAATTTGATTTTGTAATACCTCTGTGAAACATAATAAAATGGTTTATAAAATAGGTTTTCTGATAACATTTTTTGTTTTCTGTTTAATGGGGACAATGTTAACATTTGTTAGAGAAAAAATGGCCTGTAGTAGATACAACTAGTTTGATTTTTAAAATGGGGGCCAAAGCTAATCCCTGGCTTGTGAACTCTGGTGTTGTACATTGCACACAG
Seq C2 exon
GTCACCTTGGCTGTGAAGAGGACTTTGCCTGCCCACAGTGTGAATCGAGCTTTCCCAGTGAGGAAGTTCTTACTGAGCACCTTCAGAGCTTGCACCAGAAGCCCACAGGGGAGAAAGAGTTCAAATGCGAGAACTGCGGGAAGAAGTTCCCTGTGAGGCAGGCCTTGCAGAGACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023679:ENSRNOT00000009569:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.407 A=NA C2=0.136
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF134651=zf-H2C2_2=WD(100=49.2)
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:
ATATTTTCTACTTGGCAGTCGATGA
R:
CTGCCTCACAGGGAACTTCTT
Band lengths:
326-1839
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]