RetrogeneDB ID: retro_meug_1672

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold52251:150..1098(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPLP0
• Ensembl ID: ENSMEUG00000016409
• Aliases: None
• Description: ribosomal protein, large, P0 [Source:HGNC Symbol;Acc:10371]

Sequence

>retro_meug_1672
ATGCTCAGGGAAGACAGGGCTACCGGGAAATCCAATTACTTCCTCAAGATCATCCAACTTTTGGATGATTATCCAAAACG
CTTCATTTTTGGAACAGACAATGTTGGCTCCAAGCAGATGCAGCAGGTCCAGATGTCCCTCCGTGGTCAGGCCGTGGTAT
TAATGCGAAAAAACACCGTGATGCACAAAGCCATTCGTGCTCACCTGGAGAACAACCCTGCCCTGGAGAAACGGCTGCTG
CATATTTGGGGGAATGTGGGCTTCGTGTTCACCAAGGAAGATCCGACTGAGATTAGGGATATGCTTCTGGTCAATAAGGT
ACCAGCTGCTGCCCGTACTGGTGCCATTGCCCCATGTGATGTCACCGTACCCTCCCAGAACACTGGTCTGGGTCCCGAGA
AGACTTCCTTCTTCCAAGCTCTGGGTATCACCCCAAGATTTCCAGGGGCACCACTGAAATCTTGAGTGATGTGTTACTGA
TTAAGACCGAAGATAAAGTGGGTGCCAACGAGGCCACCTTGTTGAACATACTGCACGTTTCCCCGTTCTCCTTTGGGTTG
ATCTTTCAGCTGGTGTTTGACCACGGCAGCATGGGCAGCCCTGAAGCGCTGGACATCACGGAGGAGACTTTGCATCTTCG
GTTCTTAGAGGGTGCCCTTAACGTTGCCAGTGTCTGTCTGCAGATTGGCTACCCAACTGTTGCATCAGTACTCCACTAGA
TCATTAATGGGTACAAGTGGGTCTTGGTGTAGCTCTGGAGACTGAGTACACCTTCCCACTTGCTGAAAAGGTGAAGGCAT
TCCTGGCCCACCCTTCGGCATTTGCAGTGGCCGCCCCTGCAGGGGCTGCTGCTGCATCTGCTGCACCTGCTGCTCCTGCT
GCAGCCAAGTGGAAGCCACAGAAGAATGGGGGAAGTCTGATGAAGATGCGGGATTTGGTCTATTTGAT

Alignment

ORF - retro_meug_1672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKAVVLMGKNTMMRKAIRGHLE
          M.REDRAT.KSNYFLKIIQLLDDYPK.FI.G.DNVGSKQMQQ..MSLRG.AVVLM.KNT.M.KAIR.HLE
Retrocopy MLREDRATGKSNYFLKIIQLLDDYPKRFIFGTDNVGSKQMQQVQMSLRGQAVVLMRKNTVMHKAIRAHLE

Parental  NNPALEKLLPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCDVTVPAQNTGLGPEKTSFFQA
          NNPALEK.L.HI.GNVGFVFTKED.TEIRDMLL.NKVPAAAR.GAIAPCDVTVP.QNTGLGPEKTSFFQA
Retrocopy NNPALEKRLLHIWGNVGFVFTKEDPTEIRDMLLVNKVPAAARTGAIAPCDVTVPSQNTGLGPEKTSFFQA

Parental  LGIT-TKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLIIQQVFDNGSIYNPEVLDITEE
          LGIT..KISRGT.EILSDV.LIKT.DKVGA.EATLLN.L..SPFSFGLI.Q.VFD.GS...PE.LDITEE
Retrocopy LGIT<PKISRGTTEILSDVLLIKTEDKVGANEATLLNILHVSPFSFGLIFQLVFDHGSMGSPEALDITEE

Parental  TLHLRFLEGVRNVASVCLQIGYPTVASVPHSIINGYKRV-LAVAVETEYTFPLAEKVKAFLADPSAFAVA
          TLHLRFLEG..NVASVCLQIGYPTVASV.H.IINGYK.V.L.VA.ETEYTFPLAEKVKAFLA.PSAFAVA
Retrocopy TLHLRFLEGALNVASVCLQIGYPTVASVLH*IINGYKWV<LGVALETEYTFPLAEKVKAFLAHPSAFAVA

Parental  APVAAAPAAAAPAAAAPAK-VEAKEESEESDEDMGFGLFD
          AP...............AK.VEA.EE...SDED.GFGLFD
Retrocopy APAXXXXXXXXXXXXXXAK<VEATEEWGKSDEDAGFGLFD

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_1672 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1672 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 18 parental genes, and 71 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003756	2 retrocopies	retro_acar_111, retro_acar_115,
Ailuropoda melanoleuca	ENSAMEG00000005144	4 retrocopies	retro_amel_1179, retro_amel_1194, retro_amel_1377, retro_amel_847,
Canis familiaris	ENSCAFG00000010227	5 retrocopies	retro_cfam_1580, retro_cfam_224, retro_cfam_487, retro_cfam_534, retro_cfam_693,
Callithrix jacchus	ENSCJAG00000008677	3 retrocopies	retro_cjac_1693, retro_cjac_2840, retro_cjac_786,
Cavia porcellus	ENSCPOG00000021812	5 retrocopies	retro_cpor_298, retro_cpor_449, retro_cpor_475, retro_cpor_498, retro_cpor_601,
Equus caballus	ENSECAG00000015816	2 retrocopies	retro_ecab_1090, retro_ecab_585,
Felis catus	ENSFCAG00000013354	1 retrocopy	retro_fcat_441,
Gorilla gorilla	ENSGGOG00000026582	5 retrocopies	retro_ggor_1088, retro_ggor_1771, retro_ggor_472, retro_ggor_649, retro_ggor_650,
Macropus eugenii	ENSMEUG00000016409	12 retrocopies	retro_meug_1211, retro_meug_1245, retro_meug_1339, retro_meug_1410, retro_meug_1672 , retro_meug_1689, retro_meug_1789, retro_meug_1800, retro_meug_1943, retro_meug_2166, retro_meug_294, retro_meug_772,
Myotis lucifugus	ENSMLUG00000001970	11 retrocopies	retro_mluc_1016, retro_mluc_1460, retro_mluc_1503, retro_mluc_1806, retro_mluc_1966, retro_mluc_2293, retro_mluc_268, retro_mluc_497, retro_mluc_564, retro_mluc_565, retro_mluc_882,
Macaca mulatta	ENSMMUG00000009157	2 retrocopies	retro_mmul_2245, retro_mmul_939,
Mus musculus	ENSMUSG00000067274	2 retrocopies	retro_mmus_143, retro_mmus_2249,
Oryctolagus cuniculus	ENSOCUG00000005749	2 retrocopies	retro_ocun_293, retro_ocun_376,
Otolemur garnettii	ENSOGAG00000003843	4 retrocopies	retro_ogar_2184, retro_ogar_2294, retro_ogar_556, retro_ogar_713,
Petromyzon marinus	ENSPMAG00000001339	1 retrocopy	retro_pmar_6,
Pongo abelii	ENSPPYG00000005022	5 retrocopies	retro_pabe_2113, retro_pabe_3035, retro_pabe_568, retro_pabe_66, retro_pabe_749,
Rattus norvegicus	ENSRNOG00000001148	3 retrocopies	retro_rnor_1350, retro_rnor_2092, retro_rnor_2970,
Sarcophilus harrisii	ENSSHAG00000001623	2 retrocopies	retro_shar_286, retro_shar_413,