RetrogeneDB ID: retro_oana_106

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Ultra265:80655..80949(+)
• Located in intron of: ENSOANG00000006769

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOANG00000008597
• Aliases: None
• Description: None

Sequence

>retro_oana_106
TTAGATGAAGGAAAGGGGTTTCTGTTTAGGTTTAGCTGTTGATATCCTTTTGATTCTCCTTGAAAAATGTTTACAAATGA
GAATATTCCTGTTGGTCCTCATGTTTAGAGCAATGGCTCTATCTGTTTATTCCTTCTAACTGAAGACTGGACTCTAGTGC
ACAGAGGCCAATCTGTTTATCTTAAGCGTTATTAGCGTGCCCTCAGCTTCAAAGAAGAGGGGTGACCACTAGATCGTTCT
CTTTATGGTGATTCATGCCCTAGGACTCCAAAGAAGACAAAATGGTGGTGGTAT

Alignment

ORF - retro_oana_106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54. %
• Parental protein coverage: 77.52 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LYEGEKFQLLFKFSSRYPFDSPQVMFTGDNIPVHPHVYSNGHICLSILTEDWSPALSVQSVCLSIISMLS
          L.EG..F..LF.FS..YPFDSP..MFT..NIPV.PHV.SNG.ICL..LTEDW......QSV.L.......
Retrocopy LDEGKGF--LFRFSC*YPFDSP*KMFTNENIPVGPHV*SNGSICLFLLTEDWTLVHRGQSVYLKRY*RAL

Parental  SCKEKRRPPDNSFYVRTCNKNPKKTKWWYH
          S.KE...P.D.S.Y...C...PKKTKWW..
Retrocopy SFKEEG*PLDRSLYGDSCPRTPKKTKWWWY

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	8.30 RPM
SRP007412_cerebellum	0.00 RPM	10.77 RPM
SRP007412_heart	0.00 RPM	4.69 RPM
SRP007412_kidney	0.00 RPM	3.55 RPM
SRP007412_liver	0.00 RPM	1.72 RPM
SRP007412_testis	0.00 RPM	9.73 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_106 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_106 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000025939	1 retrocopy	retro_mmus_3516,
Ornithorhynchus anatinus	ENSOANG00000008597	1 retrocopy	retro_oana_106 ,
Oryctolagus cuniculus	ENSOCUG00000010245	1 retrocopy	retro_ocun_1189,
Otolemur garnettii	ENSOGAG00000027181	2 retrocopies	retro_ogar_460, retro_ogar_766,
Procavia capensis	ENSPCAG00000012043	2 retrocopies	retro_pcap_128, retro_pcap_278,