RetrogeneDB ID: retro_meug_1482

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold42146:16199..17372(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PKM
• Ensembl ID: ENSMEUG00000004506
• Aliases: None
• Description: pyruvate kinase, muscle [Source:HGNC Symbol;Acc:9021]

Sequence

>retro_meug_1482
TATCATGCTGAAACCATCAAAAATGTTCGAACAGCCACAGAGAGCTTTGCTTCTAGCCCTGTCCATTACTGACCTATTGC
TATAGCCTTGGACACCAAAGGACCAGAGATCCGAACTGGATTCATCAAGGGCAGTGGCACAGCCGAAGTAGAGCTAAAGA
AGGGTAACACTCTGAAGGTCACCTTGGATGAAGCCTATATGGAGAAATGTGATGAAAATGTCCTGTGGTTAGACTACAAA
AACATTTGCAAGGTGGTGGATGTTGGTAGCAAAGTCTTTGTGGATGATGGGCTCATTTCTCTTCTTGTGAAGGAGAAAGG
TGCCAATTTCCTTATCACTGAGGTGGAGAATGGAGGCATGCTGGGCAGCAAGAAGGGTGTCAACCTTCCTGGGGCAGCTG
TCGACTTGCCTGCTGTGTCTCAGAAAGATATCCAAGATCTTCACTTTGGATTAGAGCAAGGGGTGGATATGGTGTTTGCA
TCTTTCATCCGAAAGGCAGATGATGTCCATGCAGTCAGAAAGGTCCTAGGAGAGAAAGGCAAAAACATCAAGATCATCAG
CAAGATTGAAAACCATGAAGGAGTCCGAAGATTTGATGAGATCCTGGAAGCCAATGAGGACATCGTGGTTGCTCGGGGGG
ACCTAGGTATTGAGATCCCTGCAGAAAAGGTCTTTGTTGCTCAGAAGATGATGATTGGAAGGTGTAATAGAGCTGGGAAA
CCTGTTATTTGTGCCACTCAGATGCTCGAGAGCATGATTAAGAAGCCACGCCCCACGCAGGCTGAAGGCAGTGATGTAGC
CAATGATGTCCTGGATGGAGCTGATTGTATCATGCTATCTGGGGAGACTGCCAAAGGGGACTATCCAGTAGAAGCTATGC
GGATGCAACACTTGATTGCCCGAGAGGCAGAGGCCACCATCTTTCACACGCAGTTGTTTGAGGAGCTTCGCCGCCTGGCC
CCCGTAACCAAGGATCCCACTGAAGCTGCTGCCGTGGGTGCCGTAGATGCTTCCTTCAAGTGTTGCAGTGGGGCCATTAT
CGTTCTCACCAAGTCTGGAAGGTCTGCTTATCAGGTAGCTAGGTACCGTCCTCGGGCCCCCATCATAGCTGTTACTCGTT
CTGCTCAGGCTGCACGTCAAGCTCATCTCCACCGGGGTGTCTTTCCTGTGCTG

Alignment

ORF - retro_meug_1482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.07 %
• Parental protein coverage: 75.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YHAETIKNVRTATESFASSPVHYRPIAIALDTKGPEIRTGLIKGSGTAEVELKKGNTLKVTLDEAYMEKC
          YHAETIKNVRTATESFASSPVHY.PIAIALDTKGPEIRTG.IKGSGTAEVELKKGNTLKVTLDEAYMEKC
Retrocopy YHAETIKNVRTATESFASSPVHY*PIAIALDTKGPEIRTGFIKGSGTAEVELKKGNTLKVTLDEAYMEKC

Parental  DENVLWLDYKNICKVVDVGSKVFVDDGLISLLVKEKGANYLITEVENGGMLGSKKGVNLPGAAVDLPAVS
          DENVLWLDYKNICKVVDVGSKVFVDDGLISLLVKEKGAN.LITEVENGGMLGSKKGVNLPGAAVDLPAVS
Retrocopy DENVLWLDYKNICKVVDVGSKVFVDDGLISLLVKEKGANFLITEVENGGMLGSKKGVNLPGAAVDLPAVS

Parental  QKDIQDLHFGLEQGVDMVFASFIRKADDVHAVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMV
          QKDIQDLHFGLEQGVDMVFASFIRKADDVHAVRKVLGEKGKNIKIISKIENHEGVRRFDEILEA...I.V
Retrocopy QKDIQDLHFGLEQGVDMVFASFIRKADDVHAVRKVLGEKGKNIKIISKIENHEGVRRFDEILEANEDIVV

Parental  ARGDLGIEIPAEKVFVAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLS
          ARGDLGIEIPAEKVFVAQKMMIGRCNRAGKPVICATQMLESMIKKPRPT.AEGSDVAN.VLDGADCIMLS
Retrocopy ARGDLGIEIPAEKVFVAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTQAEGSDVANDVLDGADCIMLS

Parental  GETAKGDYPVEAVRMQHLIAREAEAAIYHRPLFESLLRCSSCT-DTADAMAVGAVEASYKCLSPALIVLT
          GETAKGDYPVEA.RMQHLIAREAEA.I.H..LFE.L.R....T.D...A.AVGAV.AS.KC.S.A.IVLT
Retrocopy GETAKGDYPVEAMRMQHLIAREAEATIFHTQLFEELRRLAPVTKDPTEAAAVGAVDASFKCCSGAIIVLT

Parental  ESGRSAYQVARYRPRAPIIAVTRSAQAARQAHLHRGVFPVL
          .SGRSAYQVARYRPRAPIIAVTRSAQAARQAHLHRGVFPVL
Retrocopy KSGRSAYQVARYRPRAPIIAVTRSAQAARQAHLHRGVFPVL

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_1482 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1482 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 13 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013504	1 retrocopy	retro_chof_1430,
Callithrix jacchus	ENSCJAG00000018473	1 retrocopy	retro_cjac_236,
Felis catus	ENSFCAG00000000653	1 retrocopy	retro_fcat_105,
Homo sapiens	ENSG00000067225	2 retrocopies	retro_hsap_210, retro_hsap_3418,
Gorilla gorilla	ENSGGOG00000005062	1 retrocopy	retro_ggor_281,
Macropus eugenii	ENSMEUG00000004506	3 retrocopies	retro_meug_1482 , retro_meug_2043, retro_meug_912,
Macaca mulatta	ENSMMUG00000023454	1 retrocopy	retro_mmul_183,
Mus musculus	ENSMUSG00000032294	8 retrocopies	retro_mmus_1402, retro_mmus_1678, retro_mmus_1754, retro_mmus_2065, retro_mmus_2066, retro_mmus_2636, retro_mmus_3509, retro_mmus_854,
Nomascus leucogenys	ENSNLEG00000013869	3 retrocopies	retro_nleu_1859, retro_nleu_2319, retro_nleu_2716,
Pongo abelii	ENSPPYG00000006613	3 retrocopies	retro_pabe_2834, retro_pabe_3645, retro_pabe_429,
Pan troglodytes	ENSPTRG00000007246	2 retrocopies	retro_ptro_2322, retro_ptro_335,
Rattus norvegicus	ENSRNOG00000011329	6 retrocopies	retro_rnor_1120, retro_rnor_2050, retro_rnor_2253, retro_rnor_2703, retro_rnor_515, retro_rnor_830,
Sarcophilus harrisii	ENSSHAG00000010300	1 retrocopy	retro_shar_90,