RetrogeneDB ID: retro_oana_13

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: 3:26524605..26525003(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EXOSC3
• Ensembl ID: ENSOANG00000000886
• Aliases: None
• Description: exosome component 3 [Source:HGNC Symbol;Acc:17944]

Sequence

>retro_oana_13
TATGTGGCGTTTCAAAGTACAACCAAACGAAACAGACCAGAAGTGCTGGCGGGAGATCTTATTTATGGTCAATTCATTGT
TGCCAATAAAGACATGGAATCAGAGATTGCTTGTATCAGCAGTGGTGGAAGAGGAAATGGAATGGGTATAATTGGACAAG
ATGGCCTTTTGCTTGAGGCTACCAAAGTAGCCTTAATTAGAAAGCTTTAGCCCCAGGATGTTAAATCATCCAGGAGATGA
GTAAACTCTACCCAGTGGAGATAACTGGAATGAATAGGAGAACATGGGGAAAAGCAAGAACCATTCAACACACTTTAATT
TTGGCAAATATTTTAGAGGCCTGTGAGTTCATGACAACCAACCAAAGAAAGCAAATATTATCTAGGTTGGCAGACAGA

Alignment

ORF - retro_oana_13 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.04 %
• Parental protein coverage: 52.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YLAFEGATKRNRPDVQVGDLIYGQFIVANKDMEPEIACISSGGKGNGMGVIGQDGLLIKAT-LGLIRKL-
          Y.AF...TKRNRP.V..GDLIYGQFIVANKDME.EIACISSGG.GNGMG.IGQDGLL..AT...LIRKL.
Retrocopy YVAFQSTTKRNRPEVLAGDLIYGQFIVANKDMESEIACISSGGRGNGMGIIGQDGLLLEATKVALIRKL<

Parental  LSPSCEIIQEMSKLFPMEIVIGMNGRIWVKAKTIQQTLILANILEACEFMTTDQRKRILARLADR
          L.P.C.IIQEMSKL.P.EI..GMN.R.W.KA.TIQ.TLILANILEACEFMTT.QRK.IL.RLADR
Retrocopy LAPGC*IIQEMSKLYPVEIT-GMNRRTWGKARTIQHTLILANILEACEFMTTNQRKQILSRLADR

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	13.69 RPM
SRP007412_cerebellum	0.05 RPM	13.95 RPM
SRP007412_heart	0.00 RPM	13.28 RPM
SRP007412_kidney	0.00 RPM	16.58 RPM
SRP007412_liver	0.00 RPM	30.56 RPM
SRP007412_testis	0.00 RPM	29.89 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_13 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_13 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000107371	1 retrocopy	retro_hsap_2504,
Gorilla gorilla	ENSGGOG00000006970	1 retrocopy	retro_ggor_1562,
Nomascus leucogenys	ENSNLEG00000003529	1 retrocopy	retro_nleu_1434,
Ornithorhynchus anatinus	ENSOANG00000000886	1 retrocopy	retro_oana_13 ,
Pongo abelii	ENSPPYG00000019055	1 retrocopy	retro_pabe_1843,
Pan troglodytes	ENSPTRG00000020952	1 retrocopy	retro_ptro_1455,