RetrogeneDB ID: retro_meug_1278

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold349905:2..1183(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RIOK3
• Ensembl ID: ENSMEUG00000006292
• Aliases: None
• Description: RIO kinase 3 [Source:HGNC Symbol;Acc:11451]

Sequence

>retro_meug_1278
TCTGAAGATGAAGGTGACTTGCAGGATACTCGCCATGATCCCTACAGAGCAGCTAAACTTGTTCTTACTCCGAAGAAGGG
TTTTATTGGAAAAGGAAAAGATATTACCACCAAAAATGATGAAGTAGTGTGTGGAAGAAAGAATACAGCATGAGTGGAAA
ATTTTACACCTGGATTCCAAGTAGGAGATAGAATTGGGATGGATTTAAAACTACCAAATCAGGTCTTCAATGCTTTAAAA
CAACATGCCTACTCTGAGGAACGTCAGAGTGCCTGTGTTCATGAGAAAAAGGAACATTCTACAGTGCAAAAAGCAGTAGA
TCATAAAACACATTTACTTATGTACAAGATGGTCAATTCTGGAATGCTGGAGACAATCACTGACTATATTAGTACAGGAA
AGGAATCTGTTGTCTTTCATACATATGGAGGGAGCATGGAAGATGAGAAAGAAGATAATAAGGTTCTACCTTCAGAATGT
GCCCTAATGGTATTTAGAACAACTCTTAATGAATTCAAGAATCGTGACAAATACATTAAGGATGATTTCAGGTTTAAAGA
TCGATTAAATATCGATTCATTGAATCCACAAAAGGTCATCCTTATGTGGGCAGAAAAAGAAATGCACAATCTAACAAGAA
TGCAAAGGGCTAGTATCTTTTGCCCAGAAGTCATAATGTTAAAGAAATACATTTTGGTCATGTCTTTTATTGGCAAACAT
CAAGTCCCAGCTCCCAAAGTGAAGGAAGTAAAACTCAGTAGTGAAGACATGAAAGAGGTCTACTATCAAACCCTCCATAT
GATGCAGCAGCTTTATCAGGAGTGCAGTCTTGTCCATGCTGATTTGAGTGAGTACAACATGCTTTGGCATGTCAAAAAGG
TCTGATTGATTGACATTAGTCATTCTGTGGAGCCAACCCATCCTCATGGTCTAGAGTTCTTGTTTCAAGATTGCAAGAAT
GTATCACAGATTTTCAGAAAGAAGGGGTAAGTGAAGCCCTTGGTGAATGAGACCTCTTCAATGCTATGTCAGGCTTAAAC
ATACCAGCAGATAATGAAGTTGATTTCCTGGCTGAGATAGAAGCTTTGGAGAAAATGAATGAAGATCATGTTCAGAAGAA
TGGAAGGAAGTCTGCTTCATTTTTAAAAGATAATGGAGGCCCACCAATAATATGTGATGAA

Alignment

ORF - retro_meug_1278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.82 %
• Parental protein coverage: 75.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SEDEVDWQDTRHDPYRAAKPVPTPKKGFIGKGKDITTKHDEVVCGRKNTARMENFAPGFQVGDGIGMDLK
          SEDE.D.QDTRHDPYRAAK.V.TPKKGFIGKGKDITTK.DEVVCGRKNTA..ENF.PGFQVGD.IGMDLK
Retrocopy SEDEGDLQDTRHDPYRAAKLVLTPKKGFIGKGKDITTKNDEVVCGRKNTA*VENFTPGFQVGDRIGMDLK

Parental  LPNQVFNALKQHAYSEERRSARVHEKKEHSTAEKAVDPKTRLLMYKMVNSGMLETITGCISTGKESVVFH
          LPNQVFNALKQHAYSEER.SA.VHEKKEHST..KAVD.KT.LLMYKMVNSGMLETIT..ISTGKESVVFH
Retrocopy LPNQVFNALKQHAYSEERQSACVHEKKEHSTVQKAVDHKTHLLMYKMVNSGMLETITDYISTGKESVVFH

Parental  AYGGSMEDGKEDSKVVPSECALKVFKTTLNEFKNRDKYIKDDFRFKDRFS--KLNPRKIIRMWAEKEMHN
          .YGGSMED.KED.KV.PSECAL.VF.TTLNEFKNRDKYIKDDFRFKDR.....LNP.K.I.MWAEKEMHN
Retrocopy TYGGSMEDEKEDNKVLPSECALMVFRTTLNEFKNRDKYIKDDFRFKDRLNIDSLNPQKVILMWAEKEMHN

Parental  LTRMQKAGISCPEVIMLKKHILVMSFIGKDQVPAPKLKEVKLSSEDMKEAYYQILHMMQKLYKECSLVHA
          LTRMQ.A.I.CPEVIMLKK.ILVMSFIGK.QVPAPK.KEVKLSSEDMKE.YYQ.LHMMQ.LY.ECSLVHA
Retrocopy LTRMQRASIFCPEVIMLKKYILVMSFIGKHQVPAPKVKEVKLSSEDMKEVYYQTLHMMQQLYQECSLVHA

Parental  DLSEYNMLWHAGKVWLIDVSQSVEPTHPHGLEFLFRDCRNVSQF-FQKGGVSEALGERELFNAVSGLNIT
          DLSEYNMLWH..KV.LID.S.SVEPTHPHGLEFLF.DC.NVSQ..FQK.GVSEALGE..LFNA.SGLNI.
Retrocopy DLSEYNMLWHVKKV*LIDISHSVEPTHPHGLEFLFQDCKNVSQI<FQKEGVSEALGE*DLFNAMSGLNIP

Parental  ADNEVDFLAEIEALEKMNEDHVQKNGRKSASFLKDDGGPPIICDE
          ADNEVDFLAEIEALEKMNEDHVQKNGRKSASFLKD.GGPPIICDE
Retrocopy ADNEVDFLAEIEALEKMNEDHVQKNGRKSASFLKDNGGPPIICDE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_1278 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1278 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008343	1 retrocopy	retro_chof_1788,
Callithrix jacchus	ENSCJAG00000020556	1 retrocopy	retro_cjac_2617,
Echinops telfairi	ENSETEG00000003689	1 retrocopy	retro_etel_2181,
Macropus eugenii	ENSMEUG00000006292	1 retrocopy	retro_meug_1278 ,
Macaca mulatta	ENSMMUG00000021478	1 retrocopy	retro_mmul_1291,
Ochotona princeps	ENSOPRG00000004803	2 retrocopies	retro_opri_1034, retro_opri_946,
Pongo abelii	ENSPPYG00000009062	1 retrocopy	retro_pabe_1011,