RetrogeneDB ID: retro_oana_39

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig182823:186..651(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOANG00000004572
• Aliases: None
• Description: None

Sequence

>retro_oana_39
TTCGCTGACTTAGGAGTCTGCAAAGAGCTCTGCGATGCCTGCCTGCAGTTGGGCTGGCGCGAGCCTACAGCTATACAAGC
AGCTACACTCCCTGCAGCCTTAAGTGGCAAGGATATCATTGGTCTAGCTGAAACAGGATCCGGTAAGACAGCTGCGTTTG
CTATACCAGTGCTTCAAGCACTCTTGGAGACCCCTCAGCGGTTGTTCTGTGTTGTTTTGGCACCAACCAGGGAACTATCG
CAACAAATTATGGAGACATTTAGAGCTTTAGGAGCATCTATAGCATTGGATGTATGTGTCATATTAGGAGGAATGGATTT
TGTGACGCAATCACTACAGTTGGCCAAAAAACCTCATGTTATTGTGGCTTCACCTGGTAGATTGGCAGATCATCTAGAAA
ACACCAAAGGGTTTGAGCTTACTAAAAGCAAATTTTTGGTACTAGACGAAGCCGATCGTTTGTTG

Alignment

ORF - retro_oana_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.48 %
• Parental protein coverage: 83.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FGALGLAPWLVEQCQQLGLRQPTPVQQSCVPAILEGRDCMGCAKTGSGKTAAFVLPILQKLSEDPYGIFC
          F..LG....L...C.QLG.R.PT..Q....PA.L.G.D..G.A.TGSGKTAAF..P.LQ.L.E.P...FC
Retrocopy FADLGVCKELCDACLQLGWREPTAIQAATLPAALSGKDIIGLAETGSGKTAAFAIPVLQALLETPQRLFC

Parental  LVLTPTRELAYQIAEQFRVLGKPLGLKDCIVVGGMDMVTQALDLSRKPHVVIATPGRLADHLRSSSTFSI
          .VL.PTREL..QI.E.FR.LG....L..C...GGMD.VTQ.L.L..KPHV..A.PGRLADHL.....F..
Retrocopy VVLAPTRELSQQIMETFRALGASIALDVCVILGGMDFVTQSLQLAKKPHVIVASPGRLADHLENTKGFEL

Parental  KKIRFLVMDEADRLL
          .K..FLV.DEADRLL
Retrocopy TKSKFLVLDEADRLL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	5.03 RPM
SRP007412_cerebellum	0.00 RPM	6.09 RPM
SRP007412_heart	0.00 RPM	8.50 RPM
SRP007412_kidney	0.00 RPM	2.37 RPM
SRP007412_liver	0.00 RPM	2.08 RPM
SRP007412_testis	0.00 RPM	1.78 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_39 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_39 was not experimentally validated.

Homology

Retrocopy orthology:

Ornithorhynchus anatinus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000011888	1 retrocopy	retro_meug_362,
Ornithorhynchus anatinus	ENSOANG00000004572	1 retrocopy	retro_oana_39 ,
Pelodiscus sinensis	ENSPSIG00000008625	1 retrocopy	retro_psin_51,