RetrogeneDB ID: retro_oana_45

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig208006:528..834(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPC1
• Ensembl ID: ENSOANG00000004153
• Aliases: None
• Description: mitochondrial pyruvate carrier 1 [Source:HGNC Symbol;Acc:21606]

Sequence

>retro_oana_45
ATGGCGGGACCCCTTAAAAATGCGACAAAAGCCGCTGGAGCTGCAACTGGAGGCAGGTACTTTTTAACAACCCACTTTTG
GGGGCCAGTGGCCAATTGGGGTTTTGTGATTGCTGGCCTGAGTGACATGCGCAAGTCGCCCGAACGTATCAGCGTTCGAA
TGTCTGGAGTGTTGTGCTTTTATAGCGTGCTGTTTATGAGATTCGCAGTGATGGTACAGCCTCGGAATTTGTTGCTGTTT
GCATGCCATTTTTGCAACGCCAACGTACAAGCAGTTCAATTTTACAGGGGATTCAAATACGAAATG

Alignment

ORF - retro_oana_45 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.94 %
• Parental protein coverage: 94.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGALVRKAADYVRSKDFRDYLMRHFWGPVANWGLPVAAINDMKKSPEIISGRMTFALCCYSLTFMRFAY
          MAG.L.............R..L..HFWGPVANWG...A...DM.KSPE.IS.RM...LC.YS..FMRFA.
Retrocopy MAGPLKNATKAAGAATGGRYFLTTHFWGPVANWGFVIAGLSDMRKSPERISVRMSGVLCFYSVLFMRFAV

Parental  KVQPRNWLLFACHATNEVAQLIQGGRLIKYRM
          .VQPRN.LLFACH..N...Q..Q..R..KY.M
Retrocopy MVQPRNLLLFACHFCNANVQAVQFYRGFKYEM

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	185.28 RPM
SRP007412_cerebellum	0.00 RPM	107.25 RPM
SRP007412_heart	0.00 RPM	746.71 RPM
SRP007412_kidney	0.00 RPM	468.72 RPM
SRP007412_liver	0.00 RPM	308.46 RPM
SRP007412_testis	0.00 RPM	151.10 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_45 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_45 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027879	1 retrocopy	retro_btau_43,
Callithrix jacchus	ENSCJAG00000012552	2 retrocopies	retro_cjac_2102, retro_cjac_4053,
Dasypus novemcinctus	ENSDNOG00000001205	1 retrocopy	retro_dnov_2139,
Homo sapiens	ENSG00000060762	1 retrocopy	retro_hsap_4675,
Myotis lucifugus	ENSMLUG00000000583	1 retrocopy	retro_mluc_28,
Mus musculus	ENSMUSG00000023861	3 retrocopies	retro_mmus_2037, retro_mmus_3420, retro_mmus_979,
Ornithorhynchus anatinus	ENSOANG00000004153	1 retrocopy	retro_oana_45 ,
Pongo abelii	ENSPPYG00000017166	1 retrocopy	retro_pabe_17,
Rattus norvegicus	ENSRNOG00000012415	3 retrocopies	retro_rnor_1111, retro_rnor_2632, retro_rnor_296,
Tursiops truncatus	ENSTTRG00000004456	1 retrocopy	retro_ttru_663,