RetrogeneDB ID: retro_ptro_335

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:122222234..122223203(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PKM
• Ensembl ID: ENSPTRG00000007246
• Aliases: None
• Description: pyruvate kinase, muscle [Source:HGNC Symbol;Acc:9021]

Sequence

>retro_ptro_335
ATGTTGAAGCCCCATAGTGAAGCCGGGACTGCCTTCATTCAGACCCAGCAGCTACATGCAGCCATGGCTGACACATTCCT
GGAGCACATGTGCCACCTGGACATTCACACACCACCCATCTCAGCCTGGAACACTGGCATCATCTGTACCATTAGCCCAG
CTTCCCAATCGGTGGAGATGTTGAAGGAGATGATTAAGTCTGGAACGAATGTGGCTTGTCTGAACTTCTCTCATGGAACT
CATGAGTACCACGTGGAGACCATCAAGAACATGTGCACAGCCACGGAAAGCTTTGCTGCTGACCCCATCCTCTACCGGCC
TGTTGCTTTGGCTCTGGATACTAAAGGACCTGAGATCCGAACTGGGCTCATCAAGGGCAGCAGCACCATGGAGGTGGGGC
TGAAGATGGGAGCCACTCTCAAAATCATGCTGGATAACACCTACATGAAAAAGTGTGACGAGAACATCCTGTGGCTGGAC
TACAAGAACATCTGCAAGGTGATGGAAGTGGGCAGCAAGATCTATGTGGATGATGGGCTTATTTCTCTCCAGGTAAAGCA
GAAAGGTGCTGACTTCCTGGTGACGGAGGTGGAAACTGGTGGTTCCTCGGGCAGCAAGAAGGGTGTGAACCTTCCTGGGG
CTGCTGTGGACTTGCCTGCTGTGTCAGAGGACATCCAGGACCTGAATTTTGGGGTCGAGCAGGATGTCGATATGGTGTTT
GCGTCGTTCATCCGCAAGGCATCTGACGTCCATGAAGTTAGGGAGGCCCTGGGAGAGAAGCGAAAGAACATCAAGATAAT
CAACACAATCGAGAATCATGTGGGGGTTCGGAGGTTTGATGAAATCCTAGAGGCCAGTGATGGGATCATGGTGGCTCGTG
GTAATCCAGGCATTGAGATTCCTGCAGAGAAGGTCTTCCTTGCTCAGAGGATGATGATTGGGCGTTGCAGCTGAGCTGGG
AAGCCTATC

Alignment

ORF - retro_ptro_335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.65 %
• Parental protein coverage: 61.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMN
          M.KPHSEAGTAFIQTQQLHAAMADTFLEHMC.LDI..PPI.A.NTGIICTI.PAS.SVE.LKEMIKSG.N
Retrocopy MLKPHSEAGTAFIQTQQLHAAMADTFLEHMCHLDIHTPPISAWNTGIICTISPASQSVEMLKEMIKSGTN

Parental  VARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATL
          VA.LNFSHGTHEYH.ETIKN..TATESFA.DPILYRPVA.ALDTKGPEIRTGLIKGS.T.EV.LK.GATL
Retrocopy VACLNFSHGTHEYHVETIKNMCTATESFAADPILYRPVALALDTKGPEIRTGLIKGSSTMEVGLKMGATL

Parental  KITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVN
          KI.LDN.YM.KCDENILWLDYKNICKV.EVGSKIYVDDGLISLQVKQKGADFLVTEVE.GGS.GSKKGVN
Retrocopy KIMLDNTYMKKCDENILWLDYKNICKVMEVGSKIYVDDGLISLQVKQKGADFLVTEVETGGSSGSKKGVN

Parental  LPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRF
          LPGAAVDLPAVSE.DIQDL.FGVEQDVDMVFASFIRKASDVHEVR..LGEK.KNIKII..IENH.GVRRF
Retrocopy LPGAAVDLPAVSE-DIQDLNFGVEQDVDMVFASFIRKASDVHEVREALGEKRKNIKIINTIENHVGVRRF

Parental  DEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPV
          DEILEASDGIMVARG..GIEIPAEKVFLAQ.MMIGRC..AGKP.
Retrocopy DEILEASDGIMVARGNPGIEIPAEKVFLAQRMMIGRCS*AGKPI

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_prefrontal_cortex	0.07 RPM	880.46 RPM
SRP007412_cerebellum	0.18 RPM	977.34 RPM
SRP007412_heart	0.03 RPM	361.03 RPM
SRP007412_kidney	0.03 RPM	355.48 RPM
SRP007412_liver	0.10 RPM	65.27 RPM
SRP007412_testis	0.11 RPM	495.83 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_335 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_335 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_335 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_210

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 22 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,
Nomascus leucogenys	ENSNLEG00000013869	3 retrocopies	retro_nleu_1859, retro_nleu_2319, retro_nleu_2716,
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,