RnoINT0078343 @ rn6
Intron Retention
Gene
ENSRNOG00000019145 | Kdm2a
Description
lysine demethylase 2A [Source:RGD Symbol;Acc:1309419]
Coordinates
chr1:219570015-219571238:-
Coord C1 exon
chr1:219571080-219571238
Coord A exon
chr1:219570231-219571079
Coord C2 exon
chr1:219570015-219570230
Length
849 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGC
5' ss Score
9.37
3' ss Seq
AAGTTCTTTTGCCTGTACAGGTC
3' ss Score
7.95
Exon sequences
Seq C1 exon
GATTAAAAGACCTCCTCCTAGCAGGCTGTTCCTGGTCTGCAGTATCTGCCCTCAGCACCTCCAGCTGCCCCCTTCTCAGGACCCTTGATCTTCGGTGGGCAGTAGGAATTAAAGACCCTCAAATTCGGGACTTGCTGACTCCACCCACAGATAAGCCAG
Seq A exon
GTATGCTCTGGGCCTGCCTCACTTACCTGTTTTAACTTTTTTTTTTTTTTTTTTTTTTTTAAGATAGAGCTTAAAATTTAAGGTCTCAGAATTAAACTATGAAAAATTGGAAGTATACAAGGCTAAAATTCAAGTGCTGGTTATGTACAAGCAAATAACTAAGCAAACAAACAGGAAGAAGTCCATTCTCTAAAATTTTTTAAAAGATTTATTGGGGTTGGGGATTTAGCTCAGTGGTAGAGCGCTTGCCTAGGAAGCGCAAAGCCCTGGGTTCGGTCCCCAGCTCCGAAAAAAAGAACCCAAAAAAAAAAAAAGATTTATTTATCTTATGTATGTGAGTACACTGTAGCTGTCTTCAGACACCAGAAGATCCCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCTCTGAGCCATTTCTCCAGTGGCTTCCCACCCCCCACCCCCTCATTTTATAAATAATAAGAATTTGGGCCCAGAGAGCATAAACCTGATCAAATTTTGCAAGACTTCTGACTCAGAGCAAAACTTTGAAAGTTTTTTTGAATGATAGATGGTAACAGAATCACAGGACTGAGGAAAGAGGGCTCATTCCACACACCACTTTGAAAGTGAGGCATTTACTCTGCCACTGAAAAGACGGAAATAATCTCTGTACATTGTTTGCTCCCTACATGAAGGGTTGAGTGTAGGCAGTTCTGCTTAACTCTGTCAAGGGGGTCCTAACCAGTGCATACTCCTGCCACTTGGGTCTTTAGTAGAGAATTAAAAGTTTTGATCTAAGTTCTTTTGCCTGTACAG
Seq C2 exon
GTCAAGACAATCGAAGCAAACTCCGGAACATGACTGACTTCCGGCTGGCAGGCCTTGACATCACCGATGCCACTCTCCGACTCATTATTCGCCACATGCCCCTTTTGTCTCGACTTGACCTCAGTCACTGCAGCCACCTTACAGATCAGTCCTCCAACCTGCTCACTGCTGTCGGGTCTTCCACTCGATACTCCCTTACAGAGCTCAACATGGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019145:ENSRNOT00000054850:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.167 A=NA C2=0.082
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
AAAGACCTCCTCCTAGCAGGC
R:
ATCGAGTGGAAGACCCGACAG
Band lengths:
343-1192
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]