RetrogeneDB ID: retro_mmul_183

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:114212246..114213869(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000004145
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.9617
• Ensembl ID: ENSMMUG00000023454
• Aliases: None
• Description: Pyruvate kinase [Source:UniProtKB/TrEMBL;Acc:F7F0E2]

Sequence

>retro_mmul_183
GGTCAGCGCCGGAGGACCTCAGCAGCCATGTCGAAGCCCCATAGTGAAGCCGGGACTGCCGTCATTCAGACCCAGCAGCT
GCACGCAGCCATGGCTGACACATTCCTGGAGCACATGTGCCGCCTGGACATTGACTCACCACCCGCCACAGCCCGGAACA
CTGGCATCATCTGTACCATTGGCCCAGCTTCCCGATCAGTGGAGACGTTGAAGGAGATGATTAAGTCTGGAATGAATGTG
GCTCGTCTGAACTTCTCTCATGGAACTCATGAGTACCACGCGGAGACCATCAAGAATGTGCGCACAGCCACGGAAGGCTT
TGCTTCTGACCCCATCCTCTACCGGCCCGTTGCTGTGGCTCTGGACACTAAAGGACCTGAGATCCGAACTGGGCTCATCA
AGGGCAGCGGCACTGCAGAGGTGGAGCTGAAGAAGGGAGCCACTCTCAAAATCACGCTGGATAACGCCTACATGGAAAAG
TGTGACGAGAACATCCTGTGGCTGGACTACAAGAACATCTGCAAAGTGGTGGAAGTGGGCAGCAAGATCTACGTGGATGA
TGGACTTATTTCTCTTCAGGTGAAGCAGAAAGGTGCTGACTTCCTGGTGACGGAGGTGGAAAATGGTGGCTCCTCGGGCA
GCAAGAAGGGTGTAAACCTTCCTGGGGCTGCTGTGGACTTGCCTGCTGTGTCGGAAAAGGACATCCAGGATCTGAAGTTT
GGGGTCGAGCAGGATGTTGATATGGTGCTTGCGTCATTCATCCTCAAGGCAGCTGATGTCCATGAAGTTAGGAAGGTCCT
GGGAGAGAAGGGAAACGACATCAAGATAATCAGCAAAATCGAGAATCATGAGGGGGTTCGGAGGTTTGATGAAATCCTGG
AGGCCAGTGATGGGATCATGGTGGCTCGTGGTGATGTAGGCATTGAGATTCCTGCGGAGAAGGTCTTCCTTGCTCAGAAG
ATGATGATTGGGCGGTGCAACCGAGCTGGGAAGCCTGTCATCTGTGCTACTCAGATGCTGGAGAGCATGATCAAGAAGCC
CCGCCCCACCCGGGCTGAAGGCAGTGATGTGGCCAATGCAATTCTGGATGGAGCCGACTGCATCATGCTGTCTGGAGAAA
CAGCCAAAGGGGACTATCCTCTGGAGACTGTGCGCATGCAGCACCTGATAGCCCGTGAAGCAGAGGCCGCCATCTACCAC
TTGCAATTATTTGAGGAACTCCACCGCCTGGCGCCCATTACCAGCGACCCCACAGAAGCCACCACCGTGGGTGCCGTGGA
GGCCTCCTTCAAGTGCTGCAGTGGGGCCATAATCGTCCCCACCAAGTCTGGCAGGTCTGCTCATCAGGTGGCCAGATACT
GCCCACGTGCCCCCATCATTGCTGGGACCCGGAATCCCCAGACAGCTCGTCAGGCCCACCTGTACTGTGGCATCTTCCCT
GTGCTGTGCAAGGACCCAGTCCAGGAGGCCTGGGCTGAGGACGTGGACCTCCGGGTGAACTTTGCCATGAATGTTGGCAA
GGCCCGAGGCTTCTTCAAGAAGGGAGATGTGGTCATTGTGCTGACCGGATGTCGCCCTGGCTCCGGCTTCACCAACACCA
TGCGTGTTGTTCCTGTGCCGTGA

Alignment

ORF - retro_mmul_183 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMN
          MSKPHSEAGTA.IQTQQLHAAMADTFLEHMCRLDIDSPP.TARNTGIICTIGPASRSVETLKEMIKSGMN
Retrocopy MSKPHSEAGTAVIQTQQLHAAMADTFLEHMCRLDIDSPPATARNTGIICTIGPASRSVETLKEMIKSGMN

Parental  VARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATL
          VARLNFSHGTHEYHAETIKNVRTATE.FASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATL
Retrocopy VARLNFSHGTHEYHAETIKNVRTATEGFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATL

Parental  KITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVN
          KITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGS.GSKKGVN
Retrocopy KITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSSGSKKGVN

Parental  LPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVHEVRKVLGEKGKNIKIISKIENHEGSKMF
          LPGAAVDLPAVSEKDIQDLKFGVEQDVDMV.ASFI.KAADVHEVRKVLGEKG..IKIISKIENHEG...F
Retrocopy LPGAAVDLPAVSEKDIQDLKFGVEQDVDMVLASFILKAADVHEVRKVLGEKGNDIKIISKIENHEGVRRF

Parental  DEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATHCIMLESMIKKPRPTRAEGSDV
          DEILEASDGIMVARGD.GIEIPAEKVFLAQKMMIGRCNRAGKPVICAT...MLESMIKKPRPTRAEGSDV
Retrocopy DEILEASDGIMVARGDVGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQ--MLESMIKKPRPTRAEGSDV

Parental  ANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVE
          ANA.LDGADCIMLSGETAKGDYPLE.VRMQHLIAREAEAAIYHLQLFEEL.RLAPITSDPTEAT.VGAVE
Retrocopy ANAILDGADCIMLSGETAKGDYPLETVRMQHLIAREAEAAIYHLQLFEELHRLAPITSDPTEATTVGAVE

Parental  ASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDL
          ASFKCCSGAIIV.TKSGRSAHQVARY.PRAPIIA.TRNPQTARQAHLY.GIFPVLCKDPVQEAWAEDVDL
Retrocopy ASFKCCSGAIIVPTKSGRSAHQVARYCPRAPIIAGTRNPQTARQAHLYCGIFPVLCKDPVQEAWAEDVDL

Parental  RVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP
          RVNFAMNVGKARGFFKKGDVVIVLTG.RPGSGFTNTMRVVPVP
Retrocopy RVNFAMNVGKARGFFKKGDVVIVLTGCRPGSGFTNTMRVVPVP

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.22 RPM	137.04 RPM
SRP007412_brain_prefrontal_cortex	2.54 RPM	581.73 RPM
SRP007412_cerebellum	0.19 RPM	121.53 RPM
SRP007412_heart	0.53 RPM	171.18 RPM
SRP007412_kidney	0.12 RPM	60.33 RPM
SRP007412_liver	0.04 RPM	9.54 RPM
SRP007412_testis	0.45 RPM	65.89 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_183 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_183 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_183 has 0 orthologous retrocopies within eutheria group .

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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,