RnoINT0078352 @ rn6
Intron Retention
Gene
ENSRNOG00000019145 | Kdm2a
Description
lysine demethylase 2A [Source:RGD Symbol;Acc:1309419]
Coordinates
chr1:219597442-219598518:-
Coord C1 exon
chr1:219598365-219598518
Coord A exon
chr1:219597558-219598364
Coord C2 exon
chr1:219597442-219597557
Length
807 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
CTCTATGCCCTGTCTTCCAGGTT
3' ss Score
10.29
Exon sequences
Seq C1 exon
GTCTTCTGGCTCATCCCCCCTACAGCCCACAACCTGGAGCTGTACGAGAATTGGCTGCTATCAGGGAAACAGGGAGACATCTTTCTGGGTGACCGGGTGTCAGATTGCCAACGAATTGAGCTCAAGCAGGGCTATACCTTCGTTATTCCCTCAG
Seq A exon
GTAAGCAAAGTGGGGAAAGTAGGTTGCTTTCTAGGTTTCTTAAAGAAAGCTGATTATGCACAGACTCTGAATTCAGTGTCAGCACGGCGTGCATGTGCATGAGCGTACAGTCAGCAGCAAACAATGTTTTCCTGCTTTAATGGAGTACATGCAGAGAATATGTATTTAAAAACAAATAAGAAATGGCTCAGTGGTTAAGAGCACTGACTGCTCTTCCAGAGGTCCTGAGTTCAATTCCCAGCAACCACGTGGTGGCTCACAACCATCTGTAATGGAATCTGATGTGCTCTTCTGGTGTGTCTGATGACAGCTATACTGTAGTCATAAACAAAGTAAATAAACCTTAAAAAAGAAAAATAGCAAAAGCAGTGCTTAATACTGGCACAATACTTCTCAAACATATACATTTGGACTGTATATTAAGCCCTGAAATTCAGAAGTTTTACTTGTGATGTGTCTTCTCTAGTGAGGAGAGCCAACTTTCCTCACCTGAGTGGGGAATGCTGAATCAGCAGTTTTAAGAGCCTGTCTTAAAAATAAACCTTGTTCCTTAGATATATACTCTCATTTAATGCTTACCACCATATAAAATATAATTTATTCTAGTTCTAAAGAAAAAAAATGAGGCTTTGAGAGGTAACTTGACCAGCCATTAAAGGAACCTGGGCTATGCATCAAGGATTTGTTTCCAAAAAAGAGAAGAATATATAATATATAATAATATATAATCTAGAAGTCTTGTACTATTCTGAAGAAACTATATTACAGTATGTGCTTTCAATGCTGACTCTATGCCCTGTCTTCCAG
Seq C2 exon
GTTGGATTCATGCTGTGTATACTCCTACGGACACATTAGTGTTTGGAGGCAATTTTTTGCATAGCTTTAACATCCCCATGCAATTAAAGATATATAGTATTGAAGATCGAACACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019145:ENSRNOT00000054850:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0237317=JmjC=FE(50.5=100)
A:
NA
C2:
PF0237317=JmjC=PD(17.8=46.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTTCTGGCTCATCCCCC
R:
ATATCTTTAATTGCATGGGGATGTT
Band lengths:
247-1054
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]