RetrogeneDB ID: retro_oana_84

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig53069:7595..8156(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAT2A
• Ensembl ID: ENSOANG00000003060
• Aliases: None
• Description: methionine adenosyltransferase II, alpha [Source:HGNC Symbol;Acc:6904]

Sequence

>retro_oana_84
ATATCGTATCAACGCCTAAAACAAGACCTCATGAAACACGTTATTAGCGTCGTTATTCCCCAAAAGTTTTTGGATGACAC
AACAGAATATTTGTTGAATCCATCAGGATCGTTTGTGCAAGGTGGTCCCATGAGTGATGCTGGCTTGACGGGTCGCAAAA
TCATAGTGGATACTTACGGAGGTTGGGGTGGCCATGGTGGCGGATGCTTCTCTGGCAAGGACGGTACCAAGGTTGATCGC
TCAGGCGCGTATTACGCCAGGATGGCGGCCAAGTCACTAGTAGCTAATGGATTCTGCCGAAGAGCACTAGTTCAAGTGTC
ATACTCCATTGGAGTAGTTGAGCCCTTGTCGCTGCATGTAAACACTTTTGGGACTTGTGCTGCAAACTTTAGTGATTCCG
ATTTGGAACGGTTGATTGTTCAGAATTTTGATTTTAGAGTTGGTTGCATCATAAATGAACTCAAACTAAAACGCCCAATT
TTTTCGAAAACAAGCGTTTTCGGGCACTTTGGCCGTGACGATGAGGATTTTACGTGGGAACGCGTAAAACCCCTGAAATT
T

Alignment

ORF - retro_oana_84 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.15 %
• Parental protein coverage: 55.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VCLDEMRDALKEKVIKAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAF
          .........L...VI..V.P.K.LD..T.Y.L.PSG.FV.GGP..DAGLTGRKIIVDTYGGWG.HGGG.F
Retrocopy ISYQRLKQDLMKHVISVVIPQKFLDDTTEYLLNPSGSFVQGGPMSDAGLTGRKIIVDTYGGWGGHGGGCF

Parental  SGKDYTKVDRSAAYAARWVAKSLVKGGLCRRVLVQVSYAIGVAHPLSISIFHYGT--SQKSERELLEIVK
          SGKD.TKVDRS.AY.AR..AKSLV..G.CRR.LVQVSY.IGV..PLS......GT.....S...L.....
Retrocopy SGKDGTKVDRSGAYYARMAAKSLVANGFCRRALVQVSYSIGVVEPLSLHVNTFGTCAANFSDSDLERLIV

Parental  KNFDLRPGVIVRDLDLKKPIYQRTAAYGHFGRD--SFPWEVPKKLKY
          .NFD.R.G.I...L.LK.PI...T...GHFGRD...F.WE..K.LK.
Retrocopy QNFDFRVGCIINELKLKRPIFSKTSVFGHFGRDDEDFTWERVKPLKF

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	251.78 RPM
SRP007412_cerebellum	0.00 RPM	247.74 RPM
SRP007412_heart	0.00 RPM	81.38 RPM
SRP007412_kidney	0.00 RPM	366.27 RPM
SRP007412_liver	0.00 RPM	31.91 RPM
SRP007412_testis	0.00 RPM	1419.07 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_84 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_84 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013959	1 retrocopy	retro_chof_30,
Echinops telfairi	ENSETEG00000007634	2 retrocopies	retro_etel_1308, retro_etel_1532,
Echinops telfairi	ENSETEG00000015680	4 retrocopies	retro_etel_1669, retro_etel_1813, retro_etel_597, retro_etel_977,
Ornithorhynchus anatinus	ENSOANG00000003060	1 retrocopy	retro_oana_84 ,
Otolemur garnettii	ENSOGAG00000026925	1 retrocopy	retro_ogar_1580,
Rattus norvegicus	ENSRNOG00000013520	2 retrocopies	retro_rnor_2032, retro_rnor_955,