DmeINT0022075 @ dm6
Intron Retention
Gene
FBgn0037659 | Kdm2
Description
The gene Lysine (K)-specific demethylase 2 is referred to in FlyBase by the symbol DmelKdm2 (CG11033, FBgn0037659). It is a protein_coding_gene from Dmel. It has 5 annotated transcripts and 5 polypeptides (1 unique). Gene sequence location is 3R:9052495..9063245. Its molecular function is described by: zinc ion binding; histone demethylase activity (H3-trimethyl-K4 specific); DNA binding; histone demethylase activity (H3-K36 specific). It is involved in the biological process described with 8 unique terms, many of which group under: anatomical structure development; regulation of protein metabolic process; negative regulation of nitrogen compound metabolic process; muscle structure development; multicellular organismal process. 51 alleles are reported. The phenotypes of these alleles manifest in: embryonic/larval somatic muscle; nucleolus. The phenotypic classes of alleles include: lethal; phenotype; lethal - all die before end of P-stage; increased mortality during development. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of low expression. Peak expression observed within 00-18 hour embryonic stages, during early pupal stages.
Coordinates
chr3R:9052495-9053759:+
Coord C1 exon
chr3R:9052495-9052627
Coord A exon
chr3R:9052628-9053535
Coord C2 exon
chr3R:9053536-9053759
Length
908 bp
Sequences
Splice sites
5' ss Seq
TTGGTAATT
5' ss Score
5.73
3' ss Seq
ACGATTTTGTGATTTTCCAGCTC
3' ss Score
8.06
Exon sequences
Seq C1 exon
CGTCATATTGAAAAAACCAGCAGAGAGGTCGGATCGCAGCGCTGCTGGATTTTTCAGCGATTCGCGTACGGAAAAAATCGAGTACGTCCGAGTGCGGATTGCCCAGAAATCCGTTTAAATAAGTGTTTATTTG
Seq A exon
GTAATTATTATTTAAAATACACACTTGTATAAGAGTGTGTGCGTTTTTGGTGCTGTGAAAAGTTTAGTGAACGGCCCCCACATTGACAGCGTATGAATTATAATTATAATTTACTTCATGGCGCAAGCGAAAAGATTGTAATTCGGAGAATGAGAAGACGAATCAGAACAAAAGCAAGGCGAACGGCAGAGCCACCACCACATATAGCACTCAAATCGCATCCGCAGCGGCGGAAATCTGACAAAAACTAGATACGAGGCGAAGTGCAAATTTAGAATTCTTATTACAAGTTCATGGGAAAGTGGCGAATATACGTGGAGCGTGATAAGTGAGCGTTTTTTGTGTGTTGAATGGCAAAACATCACGTTGACCGATGCACGAATGAGAGGGAGTATTTCGAGTACGCGTCGCCGGAGTCGAACTCACCACTCTAGTTTGTTTTTCCGCTTTCTTCGCGGCTCTCCCTCTCATCGCTCTCATTGCAGTGCAGTGGTGGAGCCTCTGGGCAGCGGCACACGCGTTGGGGGCCACCCCCCTCCGGCCGGTGAGCCACTGTACTTGCCGCGTGGTGAGTTTGCCGGCTGGGCCTCTGCTGCTGCTTCAGCTTCTGCTGGTGGGTTTCTTGTGCTCCGAGCTCTTGGGCTCCAACCTCTTGTGCTCCCTCTCATTGGTCGGCCAATCGTGTGTGAGTGAGCTTGTGCCTGTGCGCTGCTCCGCGTCGCGTGTCGGACCGTTTGTGTGTGGGAGTGTGTGCGTGTGCTGGCCGTTCAATTTGTGTGAAGTAATAAGCGTAATTAGTTTGTTGGTGCGGCGTCGGATTGCAATTCAGCTTAAAAACGCCACTAAATGTAAATGTAAACGTAAACGTCTGACGCATCATCTACATCTACGATTTTGTGATTTTCCAG
Seq C2 exon
CTCTAGTCTGGCCAATAGAGTCCGTCGAGTGGAACCAGAAACGAGCTGCAACTATAAAGCGTTAACAAAAAAGTATAAAATAGAAGGCAGCGATGTCCACCGCCGTTGAAACGGGGTCGTCGCCTGCCAAGAGCAATAGCAACAACAGTAGCAGTGGCGGCAACAACAACAACGGCAACGGCAATCTCAGTCCAAATGCAAAAGGCGTGCAGCGGCGTCAACTG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0037659:FBtr0300691:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=1.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0289915, FBpp0307734, FBpp0307735, FBpp0307736
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAACCAGCAGAGAGGTCGGAT
R:
CAGTTGACGCCGCTGCAC
Band lengths:
344-1252
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Neural diversity
- Neurogenesis
- Neuronal activity
- Splicing factor regulation (brain)
- Splicing factor regulation (SL2)