RetrogeneDB ID: retro_meug_1648

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold506728:110..861(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMEUG00000010779
• Aliases: None
• Description: None

Sequence

>retro_meug_1648
CCTGATGGGCAGATGCCAAGTGACAAGACCATTGGGGGTGGAGGTGACTCTTTCAGCACCTTCTTTAGTGAAACTGGAGC
TGGCAAGCATGTTCCCCATGCTGTGTTTGTAGACCTGGAACCAACTGCTATTGATGAAATTCAAACTGGAACCTACTGCC
AGTTTTTCCATCCTGAGCAGCTGATCACTAGCAAGGAAGATGCTGCCAATAACTACACCCGTGGACACTATACCATTGGC
AAAGAAGTAATTGACATTGTTCTGGGCAGAAGGCAGAAGCTTGCTGATCAGTGCACAGATCTTCAAGGTTTCTTGGTTTT
CCACAACTTTGGTGGTTAGACTGGCTCTGGTTTCACCTCTCTGCTGATGGAACGTCTGTCCATTGACTATGGCAAGAAGT
CCAAGCAGGAGTTCTCCATTTGCCCAGCCCCTAAGGTGTCCACAGCTGTAATGAAACCCTACAACTCTATTCTGACCACT
CATACCACCCTGGAGCACTCTAATTGTGCCTTCATGGTAGACAATGAAACCATCTATGATATGGTCACATAAACCTTGAC
ACTGAACGCTCAACCTATATTAATCTGAATTGCCTTATTAGTCAAATTGTGTCCTCCATGACTGCCTCTCTCTGATTTGA
TGGTGCCCTGAATGTTGATCTGGCAGAGTTCCAGACCAACCTGATGCCCTGTCCCCATATCCATTTCCCTCTGGCACATG
TACCCCAGTCATCTCTGCTGAAAAATCCTAC

Alignment

ORF - retro_meug_1648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.61 %
• Parental protein coverage: 55.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAAN
          PDGQMPSDKTIGGG.DSF.TFFSETGAGKHVP.AVFVDLEPT.IDE..TGTY.Q.FHPEQLIT.KEDAAN
Retrocopy PDGQMPSDKTIGGGGDSFSTFFSETGAGKHVPHAVFVDLEPTAIDEIQTGTYCQFFHPEQLITSKEDAAN

Parental  NYARGHYTIGKEIIDIVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSI
          NY.RGHYTIGKE.IDIVL.R..KLADQCT.LQGFLVFH.FGG.TGSGFTSLLMERLS.DYGKKSK.EFSI
Retrocopy NYTRGHYTIGKEVIDIVLGRRQKLADQCTDLQGFLVFHNFGG*TGSGFTSLLMERLSIDYGKKSKQEFSI

Parental  YPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDIC-RRNLDIERPTYTNLNRLISQIVSSITA
          .PAP.VSTAV..PYNSILTTHTTLEHS.CAFMVDNE.IYD.....NLD.ER.TY.NLN.LISQIVSS.TA
Retrocopy CPAPKVSTAVMKPYNSILTTHTTLEHSNCAFMVDNETIYDMV<HINLDTERSTYINLNCLISQIVSSMTA

Parental  SLRFDGALNVDLTEFQTNLVPYPRIHFPLA-TYAPVISAEKAY
          SL.FDGALNVDL.EFQTNL.P.P.IHFPLA.T..PVISAEK.Y
Retrocopy SL*FDGALNVDLAEFQTNLMPCPHIHFPLA<TCTPVISAEKSY

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_1648 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1648 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 29 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012244	1 retrocopy	retro_btau_402,
Bos taurus	ENSBTAG00000039992	1 retrocopy	retro_btau_840,
Canis familiaris	ENSCAFG00000008661	2 retrocopies	retro_cfam_960, retro_cfam_978,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Callithrix jacchus	ENSCJAG00000020874	2 retrocopies	retro_cjac_1603, retro_cjac_1861,
Dipodomys ordii	ENSDORG00000000154	3 retrocopies	retro_dord_460, retro_dord_564, retro_dord_786,
Equus caballus	ENSECAG00000009504	1 retrocopy	retro_ecab_1041,
Erinaceus europaeus	ENSEEUG00000004068	1 retrocopy	retro_eeur_669,
Echinops telfairi	ENSETEG00000010296	2 retrocopies	retro_etel_1816, retro_etel_1993,
Felis catus	ENSFCAG00000024852	1 retrocopy	retro_fcat_361,
Felis catus	ENSFCAG00000027277	1 retrocopy	retro_fcat_596,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Homo sapiens	ENSG00000123416	1 retrocopy	retro_hsap_808,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648 , retro_meug_2174,
Macropus eugenii	ENSMEUG00000011167	4 retrocopies	retro_meug_1121, retro_meug_157, retro_meug_1616, retro_meug_1964,
Microcebus murinus	ENSMICG00000000804	1 retrocopy	retro_mmur_103,
Monodelphis domestica	ENSMODG00000015206	2 retrocopies	retro_mdom_1632, retro_mdom_348,
Mus musculus	ENSMUSG00000023004	6 retrocopies	retro_mmus_1562, retro_mmus_1607, retro_mmus_1742, retro_mmus_1987, retro_mmus_3297, retro_mmus_3327,
Mus musculus	ENSMUSG00000043091	1 retrocopy	retro_mmus_843,
Oryctolagus cuniculus	ENSOCUG00000028032	1 retrocopy	retro_ocun_111,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pan troglodytes	ENSPTRG00000012950	1 retrocopy	retro_ptro_2158,
Pteropus vampyrus	ENSPVAG00000004646	1 retrocopy	retro_pvam_929,
Pteropus vampyrus	ENSPVAG00000010798	1 retrocopy	retro_pvam_1019,
Rattus norvegicus	ENSRNOG00000003597	1 retrocopy	retro_rnor_2819,
Rattus norvegicus	ENSRNOG00000015544	3 retrocopies	retro_rnor_1193, retro_rnor_2260, retro_rnor_960,
Sus scrofa	ENSSSCG00000000190	2 retrocopies	retro_sscr_380, retro_sscr_702,
Ictidomys tridecemlineatus	ENSSTOG00000019497	1 retrocopy	retro_itri_203,
Tursiops truncatus	ENSTTRG00000010042	1 retrocopy	retro_ttru_531,