RetrogeneDB ID: retro_cjac_236

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:122148094..122149690(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022504
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PKM
• Ensembl ID: ENSCJAG00000018473
• Aliases: None
• Description: pyruvate kinase, muscle [Source:HGNC Symbol;Acc:9021]

Sequence

>retro_cjac_236
ATGTCGAAGCCCCATAGTGAAGCCGGAACTGCCTTCATTCAGACGCAGCAGCTGCATGCAGCCATGGCTGACACATTCCT
GGAGCACATGTGCCGCCTGGACATTGACTCACCACCCATCACAGCCCGGAACACTGGCATCATCTGTACCATTGGCCCAG
CTTCCCGATCGGTGGAGACGTTGAAGGAGATGATTAAGTCTGGAATGAATGTGGCTCGTCTGAACTTCTCTCATGGAACT
CATGAGTACCATGCGGAGACCATCAAGAATGTGCGTGCAGCCACGGAAAGCTTTGCTTCTGACCCCATCCTCTACCGGCC
CGTTGCTGTGGCTCTGGACACTAAAGGACCTGAGATCCGAACTGGCCTCATCAAGGGCAGCGGCACCGCAGAGGTAGAGC
TGAAGAAGGGAGCCACTCTCAAAATCACGCTGGATAACGCCTACATGGAGAAGTGTGACGAGAACATCCTGTGGCTGGAC
TACAAGAACATCTGCAAGGTGGTGGAAGTGGGCAGCAAGATCTACGTGGATGATGAGCTTATTTCTCTCCAGGTGAAGCA
GAAAGGTGCTGACTTCCTGGTGACAGAGGTGGAAAATGGTGGCTCCTTGGGCAGCAAGAAGGGTGTGAACCTTCCTGGGG
CTGCTGTGGACTTGCCTGCTGTGTCAGAGAAGGACATCCAGGACCTGAAGTTTGGGGTTGAGCAGGATGTTGATATGGTG
TTTGCGTCATTCATCCGCAAGGCAGCCGATGTCCATGAAGTGAGGAAGGTCCTGGGAGAGAAGGGGAAGAACATCAAGAT
AATCAGCAAAATCGAGAATCATGAGGGGGTTCGGAGGTTTGATGAAATCCTGGAGGCCAGTGATGGGATCATGGTGGCTC
GTGGTGATCTAGGCATTGAAATTCCTGCAGAGAAGGTCTTCCTTGCTCAGAAGATGATGATTGGGCAGTGCAACCGAGCT
GGGAAGCCTGTCATCTGTGCCACTCAGATGCTGGAAAGCATGATCAAGAAGCCCCGCCCCACCCGGGCTGAGGGCAGTGA
TGTGGCCAATGCAGTCCTGGATGGAGCTGACTGTATCATGCTGTCTGGAGAGACAGCCAAAGGGGACTATCCTCTAGAGG
CCGTGCGCATGCAGCACCTGATTGCCCGTGAGGCAGAGGCCGCCATCTACCACTTGCAATTATTTGAGGAACTCCGCCAC
CTGGCGCCCATTACCAGCGACCCCACAGAAGCCACCGCCGTGGGCGCCGTGGAGGCCTCGTTCAAGTGCTGCAGTGGGGC
CATAATCGTCCTCACCAAGTCTGGCAGATCTGCTCACCAGGTGGCCAGATACCGCCCACGTGCCCCCATCATTGCTGTGA
CACGGAATGCCCAGACAGCTCGTCAGGCTCACCTGTACCGTGGTATCTTCCCTGTGCTGTGTAAGGACCCCATCCAGGAG
GCCTGGGCTGAGGATGTGGACCTCCGGGTGAACTTGGCCATGAATGTTGGCAAGGCCCGAGGCTTCTTCAAGAAGGGAGA
TGTGGTCATTGTGCTGACTGGGTGGCGCCCTGGCTCCGGCTTCACCAACACCATGCGTGTTGTTCCTGTGCCGTGA

Alignment

ORF - retro_cjac_236 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.44 %
• Parental protein coverage: 99.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMN
          MSKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMN
Retrocopy MSKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMN

Parental  VARLNFSHGTHEYHAETIKNVRAATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATL
          VARLNFSHGTHEYHAETIKNVRAATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATL
Retrocopy VARLNFSHGTHEYHAETIKNVRAATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATL

Parental  KITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVN
          KITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDD.LISLQVKQKGADFLVTEVENGGSLGSKKGVN
Retrocopy KITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDELISLQVKQKGADFLVTEVENGGSLGSKKGVN

Parental  LPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVHEVRKVLGEKGKNIKIISKIENHEGVRRF
          LPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVHEVRKVLGEKGKNIKIISKIENHEGVRRF
Retrocopy LPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVHEVRKVLGEKGKNIKIISKIENHEGVRRF

Parental  DEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVAN
          DEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIG.CNRAGKPVICATQMLESMIKKPRPTRAEGSDVAN
Retrocopy DEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGQCNRAGKPVICATQMLESMIKKPRPTRAEGSDVAN

Parental  AVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEAS
          AVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELR.LAPITSDPTEATAVGAVEAS
Retrocopy AVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRHLAPITSDPTEATAVGAVEAS

Parental  FKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNAQTARQAHLYRGIFPVLCKDPIQEAWAEDVDLRV
          FKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNAQTARQAHLYRGIFPVLCKDPIQEAWAEDVDLRV
Retrocopy FKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNAQTARQAHLYRGIFPVLCKDPIQEAWAEDVDLRV

Parental  NLAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP
          NLAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP
Retrocopy NLAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP

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
SRP051959_colon	0.29 RPM	76.24 RPM
SRP051959_heart	0.35 RPM	129.36 RPM
SRP051959_kidney	0.20 RPM	52.51 RPM
SRP051959_liver	0.02 RPM	7.56 RPM
SRP051959_lung	0.11 RPM	55.89 RPM
SRP051959_lymph_node	0.37 RPM	64.13 RPM
SRP051959_skeletal_muscle	1.05 RPM	397.43 RPM
SRP051959_spleen	0.15 RPM	42.71 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_236 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_236 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_236 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,