RnoINT0078341 @ rn6
Intron Retention
Gene
ENSRNOG00000019145 | Kdm2a
Description
lysine demethylase 2A [Source:RGD Symbol;Acc:1309419]
Coordinates
chr1:219572404-219575068:-
Coord C1 exon
chr1:219574359-219575068
Coord A exon
chr1:219572568-219574358
Coord C2 exon
chr1:219572404-219572567
Length
1791 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
ATTCTCTTCCCTCTTAACAGGTG
3' ss Score
11.96
Exon sequences
Seq C1 exon
AAGCGGAAAATAGAAGAGAGTGATGAAGAAGCTGTACAAGCCAAAGTCCTACGGCCCCTGAGGAGCTGCGAGGAGCCTCTCACACCCCCGCCTCACTCACCTACTTCCATGCTGCAGCTCATCCACGACCCGGTTTCTCCCCGGGGTATGGTGACTCGGTCATCCCCTGGGGCTGGCCCCAGCGACCACCACAGTGCCAGCCGTGATGAACGCTTCAAACGGCGGCAGTTGCTGCGGCTACAAGCCACAGAGCGCACCATGGTACGGGAAAAGGAGAACAATCCCAGCGGCAAAAAGGAGCTGTCTGAAGTTGAGAAAGCCAAGATCCGGGGATCGTACCTCACTGTCACGCTACAGAGGCCCACCAAAGAGCTCCACGGGACATCCATTGTGCCCAAGCTGCAGGCCATCACGGCCTCCTCTGCCAACCTTCGCCCTAACCCCCGTGTGCTAATGCAGCACTGCCCAGCCCGGAACCCCCAGCGTGGGGATGAGGAGGGGCTTGGGGGAGAGGAGGAGGAAGAGGAGGAGGAGGAGGAAGATGACAGTGCAGAGGAGGGGGGTGCAGCAAGGCTGAATGGCCGGGGCAGTTGGGCTCAGGATGGAGACGAAAGCTGGATGCAGCGGGAGGTCTGGATGTCTGTCTTCCGCTACCTCAGCCGCAGAGAACTTTGTGAATGTATGCGAGTGTGCAAGACGTGGTATAAATG
Seq A exon
GTGAGCAGGGATACAGGGGTCAGGAACGGGCAGGGGGTAGGTAACAGGGCTTCTGTGTGTACCTTGATGTCTGTGGGTATCAGACCGCCTCTGTGGGTGCTGTTAAAGATGTAGTCCATTGTACCTGCATATGTTAGGGGAATTGGAGCCTTTCGTCTTCTGCCAGCTCATTGTTTCCCTGTTTCAACTGGGGGGAGGGAAACCAATTTAAGGGGTGGATTTGTACAGTTTGTGCTAAAACTTACTTAGGGTCTTATAGGTTGTGAGCTTGTTTTCCCTCCCCTAACTTACCATGTGCTAGTTGAGATTCTGAGACGAGCTATGATTTCACCAAGAGGAGTGGCAAACTTTCCAAAATGAATTTGAAGGTGCTCCTAATATTCCCATTTTTAGTACTCTTTGGTCTCCCCTTCTGTGTTTGCTTCCAGTTTTAACTATCCCTCAAACTTGAATTTTTCCTTTCTTCAACAAGGAGAGCCCGTTTCTGAAGCTTAAGACTTAACTATCCTTCCTAATGAAACATTTCTCCGCCGGTTCAACAGACATTTAGTGGGAAAGTCCCTAGAGCTAATGAATGAAGAGATTGCTACGGAGCACCTTGAGGTTTAAGGGTGTATAATTTTTTTATTTTGGTCACACTCTATTACTGTTATTTCCAAAATCAGGTGTCTTGACCAGAAATATATGTCTGGAAACTTGTCAAAGTATGGTAGTGCCAGAGTGTGGTATTACATACATGATGCCAGCATTCAGGAGACACAGGCAGGAAGATCTGCAGTTTGGGGTGAGCAAGGGCTGTATAGCCCCAGACCAATCTGTGCTAAAGCATGAGAAGTAAAGAAAAGCAGATCCCCAGGCCTGCTAAATCAGAGCCTCTGGGGTGGGTCTGATGTAGTGTGTATTTTGTTTGGGTTTTTCTTTTTTTTTATTTAAGGACTCCTACCATCAACAGTGTGCTATCAGTGAGATTTTTGTCAATTGTAATACCTTTGCCAGTACAAATCTTACTTCTTGACTTAGAATTTGTGACCTACTCATATTACATTTTTTTTGGTCAAGCAAGTAGGCTTCCTAGTCTCTAATCCTTGGTTTCCAGGCCAGGGCACATAAGACTCCCAATACATATTTCCTTGTGTTCTGCCAGGCAGGCTGAGCTCAGGAGTGGAGATTACATTGTAGAGTGTGGTAGAAAGACCTCTCACTTTCAGTTTTGGATGGACTGGCAAGATGTTAAGCTAGCAGGGAAGCAAATGCCTTAGGGTGGAAGAGAGCTGTCCAGGCTGAGAGAAAGCGTCACTTGGCCTGTGACAGTAATAGGCTCAAGGCAAGATGTGATAGCGTTGGGTAGATCCTTCATCTCCCTCAGCTCCATGTAACTACAACTAACATGGGAAAGAATCAAGCTATGAAATTCTAGACAGTAAGAGGTCAGTCTTGTAACCAAGTTGAAGATTAAAGTCTATTTCTAAATATTGTTGAAATGTTTCTGTACACTATATAATAGGAGCCACACCATTTTAGTACAAAGGAAGAGAATACAGTATACCATTGTATAAACATGCCAAACCCCGTGCCCTGCCTATCCTGGATTTGCAAAGTGTCTAGTTTTTTTGGTTTTTTTTTTTTAAAGGGCAGTTTTTTGCCTGACTCTGAGGTAGTGATTTCTGGTTTTCTACAGGAAAACTTACAGGAATGACCTTCAGGTATTTACCAGAAGCCTTTTAGCAGAGTGCCTTGGGAGCATCTTTGACAGTAATATCAAGTTAGTTAAATTCTCTTCCCTCTTAACAG
Seq C2 exon
GTGCTGTGACAAACGACTTTGGACAAAAATTGACTTGAGTAGGTGTAAGGCCATCGTGCCCCAGGCTCTCAGTGGCATCATCAAGCGGCAGCCAGTAAGCCTGGACCTTAGTTGGACTAACATCTCCAAAAAGCAGCTGACATGGCTGGTCAATAGGCTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019145:ENSRNOT00000054850:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.795 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064628=F-box=PU(72.3=14.3)
A:
NA
C2:
PF0064628=F-box=PD(25.5=21.4)
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:
CCTAACCCCCGTGTGCTAATG
R:
GATGATGCCACTGAGAGCCTG
Band lengths:
357-2148
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]