RetrogeneDB ID: retro_oana_113

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Ultra380:3710183..3710510(+)
• Located in intron of: ENSOANG00000011096

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOANG00000002736
• Aliases: None
• Description: None

Sequence

>retro_oana_113
GACCTGAAGACCGACGGCTTCAGCCTCGACACCTGCCGGAGCATAGTGTCCGTCATGGACAACGACACCACCGGCAAGCT
GGGCTTCGAAGAATTCAAGTATCTGTGGAACAACATCAAAAAGTGGCAGTGCGTTTACAAGCAATATGACATTGATCACG
TGGGGACCCTGGGAAAGACCCAGCTACCCGGGGCGCTGCAGGCCGCTGGCTTCCAGCTGAACGAGCAGCTCTATCAGATG
ATCGTCCGCAGGTATTCCGACGAAGACGGGAGCATGGACTTCAACAACTTCATCAGTTGCCTCGTGCGCCTGGACGCCAT
GTTCCGC

Alignment

ORF - retro_oana_113 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.65 %
• Parental protein coverage: 90.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQCIYKQFDADRSGTIGSSELPGAFEAAG
          DLKTDGF..DTCRS.V.VMD.DTTGKLGFEEFKYLWNNIKKWQC.YKQ.D.D..GT.G...LPGA..AAG
Retrocopy DLKTDGFSLDTCRSIVSVMDNDTTGKLGFEEFKYLWNNIKKWQCVYKQYDIDHVGTLGKTQLPGALQAAG

Parental  FRLNEQLYQMIIRRYSDEDGNMDFDNFISCLVRLDAMFR
          F.LNEQLYQMI.RRYSDEDG.MDF.NFISCLVRLDAMFR
Retrocopy FQLNEQLYQMIVRRYSDEDGSMDFNNFISCLVRLDAMFR

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	0.09 RPM	87.69 RPM
SRP007412_cerebellum	0.05 RPM	76.64 RPM
SRP007412_heart	0.00 RPM	71.38 RPM
SRP007412_kidney	0.00 RPM	52.41 RPM
SRP007412_liver	0.09 RPM	17.00 RPM
SRP007412_testis	0.36 RPM	34.04 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_113 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_113 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009594	1 retrocopy	retro_cjac_2940,
Homo sapiens	ENSG00000126247	1 retrocopy	retro_hsap_98,
Macaca mulatta	ENSMMUG00000000249	2 retrocopies	retro_mmul_1334, retro_mmul_1567,
Mus musculus	ENSMUSG00000001794	1 retrocopy	retro_mmus_80,
Ornithorhynchus anatinus	ENSOANG00000002736	1 retrocopy	retro_oana_113 ,
Rattus norvegicus	ENSRNOG00000045747	2 retrocopies	retro_rnor_1447, retro_rnor_2145,
Sus scrofa	ENSSSCG00000030149	2 retrocopies	retro_sscr_495, retro_sscr_73,