RetrogeneDB ID: retro_oana_114

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Ultra40:333813..334689(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL15
• Ensembl ID: ENSOANG00000007286
• Aliases: None
• Description: mitochondrial ribosomal protein L15 [Source:HGNC Symbol;Acc:14054]

Sequence

>retro_oana_114
ATTGGCAGTCTGGCTGGGTCATGGCAGGTCCTGGACCTGCTTCAGACCCTGCTGCGCATTAGCCTGACCAACCCGATGCC
CACCCTTGAGTCCAAGAGGATGGATAGAAGACAGAGAGGAAGGCGAAGGGGTAGATTATGTGGCAAAGGGTATAAAGTTC
AGAGGCATAGGGGAAACCGTTCCTGTTTAGGTTTTGAGAGAGGTTATACCTTGCTTTTTCTGCATCTCCCAATATATGTA
TTCAGTGACAGTTTCTGGTGTCAGCATGTGCCTCTAGGTCTTAGGGGACTGCAGTACCTTATGGACTTGGTCCAAGTCCA
CCCTACTCATTCAGTTGATTTGACCCAGTATTTCATGCGAAGGGCATGGCAATCCAGCGCATGAAGGTAGACTACAGGAT
CCATTTAGTAGAGGAGGGTGTAGGTACCTTCGATGCTAAAGTAAATGTTGAGGTTCAGTTAGATTCAGAACTGGCCAGTG
TGGCAATTGAAAAAAATGGCAACACTATTACAAACTCCTTCTATGATCTGATAAGCGTGGTAATTCTTTGCAAACCTATT
CCCTTTTGTGTGTGTGTGGAAAGTCTATTCCAAAGCACATGCTCCTCCATGAAGAGTTGGTTTAGTACTACACGGATATC
AGGTTTTGGGGTTACCTGGTGGATCCAGCCAAGCTTCCTGAAGCCAGACATAACTAGCCAGAATATATGGCTACATTTTG
CCAGGTATCACTAAGGATGAACTTTTCAAAATGCTAAGCACCCGCAAAGACCCAAGGCCGATTTTCTTTGGTTTTGTTCC
AGGTTAGGTGGTGAATATACCCAAACAGAAAATCTTGAAGTCTACAGATGAAAATCTATTGATGTACTATAGCTCT

Alignment

ORF - retro_oana_114 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.73 %
• Parental protein coverage: 99.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VGVVMAGGGALDLLRALPRVSLANLRPSPGAKKAEKRRRGRRRGRKCGRGHKGQRQRGTRPRLGFEGGQT
          .G........LDLL..L.R.SL.N..P....K....R.RGRRRGR.CG.G.K.QR.RG.R..LGFE.G.T
Retrocopy IGSLAGSWQVLDLLQTLLRISLTNPMPTLESKRMDRRQRGRRRGRLCGKGYKVQRHRGNRSCLGFERGYT

Parental  PFYLRIPKYGFNEGHSFRRQYPPLSLKRLQYLIDLGRIDPTQPVDLTQ-LVNARGLVIQPMKRDYGVQLV
          ...L..P.Y.F....SF..Q..PL.L..LQYL.DL....PT..VDLTQ....A.G..IQ.MK.DY...LV
Retrocopy LLFLHLPIYVFSD--SFWCQHVPLGLRGLQYLMDLVQVHPTHSVDLTQ<VFHAKGMAIQRMKVDYRIHLV

Parental  EEGADIFKAKVNIEVQLASELAIAAIEKNGGVITTSFYDPISLGILCKPVPFFMC-GKPIPKRMLPP-EE
          EEG...F.AKVN.EVQL.SELA..AIEKNG..IT.SFYD.IS..ILCKP.PF..C..K...K...PP.EE
Retrocopy EEGVGTFDAKVNVEVQLDSELASVAIEKNGNTITNSFYDLISVVILCKPIPFCVC>WKVYSKAHAPP>EE

Parental  LVPYYTDARFRGYLADPAKLSEARLE-LAKKYGYILPDITKDELFKMLSTRKDPRQIFFGLAPGWVVNMA
          LV.YYTD.RF.GYL.DPAKL.EAR...LA..YGYILP.ITKDELFKMLSTRKDPR.IFFG..PG.VVN..
Retrocopy LV*YYTDIRFWGYLVDPAKLPEARHN<LARIYGYILPGITKDELFKMLSTRKDPRPIFFGFVPG*VVNIP

Parental  DKKILKPTDQNLLKYYSS
          ..KILK.TD.NLL.YYSS
Retrocopy KQKILKSTDENLLMYYSS

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	50.78 RPM
SRP007412_cerebellum	0.00 RPM	43.77 RPM
SRP007412_heart	0.00 RPM	40.03 RPM
SRP007412_kidney	0.00 RPM	63.07 RPM
SRP007412_liver	0.00 RPM	45.20 RPM
SRP007412_testis	0.00 RPM	65.71 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_114 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_114 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 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001174	1 retrocopy	retro_btau_324,
Canis familiaris	ENSCAFG00000006988	2 retrocopies	retro_cfam_1573, retro_cfam_511,
Choloepus hoffmanni	ENSCHOG00000005299	3 retrocopies	retro_chof_1379, retro_chof_1719, retro_chof_746,
Callithrix jacchus	ENSCJAG00000016719	1 retrocopy	retro_cjac_2230,
Dasypus novemcinctus	ENSDNOG00000017664	1 retrocopy	retro_dnov_364,
Erinaceus europaeus	ENSEEUG00000001454	2 retrocopies	retro_eeur_128, retro_eeur_707,
Echinops telfairi	ENSETEG00000001724	1 retrocopy	retro_etel_1304,
Mustela putorius furo	ENSMPUG00000010533	1 retrocopy	retro_mputfur_149,
Mus musculus	ENSMUSG00000033845	2 retrocopies	retro_mmus_1709, retro_mmus_3534,
Ornithorhynchus anatinus	ENSOANG00000007286	1 retrocopy	retro_oana_114 ,
Otolemur garnettii	ENSOGAG00000003768	1 retrocopy	retro_ogar_534,
Ochotona princeps	ENSOPRG00000000921	2 retrocopies	retro_opri_241, retro_opri_364,
Rattus norvegicus	ENSRNOG00000008566	2 retrocopies	retro_rnor_1344, retro_rnor_2785,
Sus scrofa	ENSSSCG00000030578	1 retrocopy	retro_sscr_617,
Tarsius syrichta	ENSTSYG00000014106	1 retrocopy	retro_tsyr_37,
Tursiops truncatus	ENSTTRG00000011844	2 retrocopies	retro_ttru_1139, retro_ttru_733,