RetrogeneDB ID: retro_meug_1938

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold73483:4401..5746(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ME3
• Ensembl ID: ENSMEUG00000011923
• Aliases: None
• Description: malic enzyme 3, NADP(+)-dependent, mitochondrial [Source:HGNC Symbol;Acc:6985]

Sequence

>retro_meug_1938
GCTAACTTTGACAGATACTTTCTTTTAATGGACCTTCAGGATGGAAAAGAAAAGCTTTCCTATTAAGTACTGACTTCTGA
CACTGAGAAATTCAGGCCTATTGCTTATACACCCACAATAGGAGTGACTTGCCAGCAGGTTGGCATAACATTTCAGAGGC
CAAGAGGTCTCTTTATCAGTATCCATGACCAAGGTCACATTGCTACATTGCTTAAGTCAGGGCCTGAAGATGTTGTCAAG
GCTTTTGTGGTGACTGATGAAGAATGGATCCTTGGCTTGGGTGATTTTGGCTGCAATGGAATGAGCATTCCAGTTGGGAA
ACCAGCATGTATACTGCCTGTGAAGGGGTGAATCCTCAAGAGTGTCTGCCTGTCATTCTCGATATGGGAACTGATAATGA
CAAGTTCCTAAAAGATCCTTTATATATTGGACTGAGACAGAAAAGAGTGAGAAGACATGATTATGACTTTTTGGATGAAT
TCATGGAGGCAGTTACTTCCAGGTTTGGAATGAATTGCCTTATTCAGGTGAGGATTTTGACAATGCAAATGCATTTCATC
TCTTGGAGAAGTACCAAAACAAATGTTGCACATTCAATAATGACATTTAAAGAACAGCATATGTTGCAGTTGCAGGTCTC
CTTGTAGCTCTCTGCACATTACTCAGAACTCTGTCTGATCACACAATTCTATTCCAAAGAGCTGGAGAGGTTGCCCTGGG
GATTGCAAACCTTATCATCATGGCCATGGAAAAAGAAGGGATATCCAAGAAAAAAACTATTGAAACGATATGGCTGGTTG
ACTCAAAAAGATTAATAGTTAAAGGAATTGCTTCTTTAACATGTAAAAAAGAGAAAATTGTCCATGAACATCATGAAATG
AATAACCTTGAAGAGATTTTCTGAGAAATAAAGCCAACTGCCCTCATAGGAGTTGCTGCAGTTGGTGGTACTTTCACAGA
ACAGATTCTCAAAGACATGGCTTCCTTCAATGAGTGACCCATCATTTTTGCTCTAAGTAATCCAACAAGCAAAGAAGAAT
GTTCTGCAGAGCAGTGCTACTGAGCGACAGAGGAATGTGGCATTTTTGTGAGTGGCAGTTCATTTGATCATGTCACTCTT
CCAGATAGATGGACCTTCTATCCTGGCCAAGGCAACAATTCCTGTGTATTTTCCAGAATAGCACTTGGTGTTGTAGCATG
TGGATTGAGGCACATCACTGATAAAATCATTCTCACTACTGCTGAGGTTACGGCTCAGGAAATATGAAGAAAACACTTGA
AAGATGGTCATCTATATCCTCCTTTGAATACCATTCAAGATGTTTCCTTGAAAATTGCAGTGAAG

Alignment

ORF - retro_meug_1938 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.6 %
• Parental protein coverage: 75.13 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SDLDKYIILMTLQDRNEKLFYRVLTSDVEKFMPIVYTPTVGLACQQYGLTFRRPRGLFITIHDKGHIATM
          ...D.Y..LM.LQD..EKL.Y.VLTSD.EKF.PI.YTPT.G..CQQ.G.TF.RPRGLFI.IHD.GHIAT.
Retrocopy ANFDRYFLLMDLQDGKEKLSY*VLTSDTEKFRPIAYTPTIGVTCQQVGITFQRPRGLFISIHDQGHIATL

Parental  LNSWPEDNIKAVVVTDGERILGLGDLGCYGMGIPVGKLA-LYTACGGVNPQHCLPVLLDVGTNNEALLKD
          L.S.PED..KA.VVTD.E.ILGLGD.GC.GM.IPVGK.A..YTAC.GVNPQ.CLPV.LD.GT.N...LKD
Retrocopy LKSGPEDVVKAFVVTDEEWILGLGDFGCNGMSIPVGKPA<MYTACEGVNPQECLPVILDMGTDNDKFLKD

Parental  PLYIGLKHKRVRGKEYDELIDEFMQAVTNKFGINCLIQF-EDFANANAFRLLHKYRNKYCMFNDDIQGTA
          PLYIGL..KRVR...YD...DEFM.AVT..FG.NCLIQ..EDF.NANAF.LL.KY.NK.C.FN.DI..TA
Retrocopy PLYIGLRQKRVRRHDYD-FLDEFMEAVTSRFGMNCLIQV<EDFDNANAFHLLEKYQNKCCTFNNDI*RTA

Parental  SVAVAGILAALRITKNKLSNHVFVFQGAGEAAMGIAHLIVMALEKEGIPKAEATKKIWMVDSKGLIVKGR
          .VAVAG.L.AL......LS.H...FQ.AGE.A.GIA.LI.MA.EKEGI.K......IW.VDSK.LIVKG.
Retrocopy YVAVAGLLVALCTLLRTLSDHTILFQRAGEVALGIANLIIMAMEKEGISKKKTIETIWLVDSKRLIVKGI

Parental  SHLNHEKEVFAQDHSEVNTLEEVVRQVKPTALIGVAAVAGAFTDQILKDMASFNKRPIIFALSNPTSKAE
          ..L...KE.....H.E.N.LEE.....KPTALIGVAAV.G.FT.QILKDMASFN..PIIFALSNPTSK.E
Retrocopy ASLTCKKEKIVHEHHEMNNLEEIF*EIKPTALIGVAAVGGTFTEQILKDMASFNE*PIIFALSNPTSKEE

Parental  CTAEKCYQLXXGRGIFASGSPFDKVTLEDGRTFFPGQGNNAYVFPGVALGIISCGVRHIPDEIFLLTAEH
          C.AE.CY......GIF.SGS.FD.VTL.D..TF.PGQGNN..VF...ALG...CG.RHI.D.I.L.TAE.
Retrocopy CSAEQCY*ATEECGIFVSGSSFDHVTLPDRWTFYPGQGNNSCVFSRIALGVVACGLRHITDKIILTTAEV

Parental  IAQEVSDEHLTQGRLYPPLSTIRDVSLRIAVK
          .AQE....HL..G.LYPPL.TI.DVSL.IAVK
Retrocopy TAQEI*RKHLKDGHLYPPLNTIQDVSLKIAVK

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_1938 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1938 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000011923	1 retrocopy	retro_meug_1938 ,