RetrogeneDB ID: retro_ptro_2322

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:6007758..6008642(+)
• 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_2322
ATGTTGAAGCCCCATAGTGAAGCCAGGGCTGCCTTCATTCAGACCCAGCAGCTGCACGCAGCCATGGCTGACACATTCTT
GGAGCACATGTGCTGCCTGGACACTGACTCGCCACCCATCACAGCCTGGAGCACTGGCATCATCTGTACTATGGGCCCGG
CTTCCCCATTGTTAGAGATGCTGAAGAAAACGATTAAGTCTGGAATGAATGTGGCTCATCTGAACTCTCATGGAGCCCAT
GAGTACCATACAGAGACCATCAAGAACGTGCGCACAGCCACGGAAAGCTTTGCTTCTGACTCCATCCTCTACCAGCCCAT
TGCTGTGGCTCCAGACACTAAAGGACCTGAGATCCCAGCTGGGCCCGTCAAGGGCAGCGGCACTGCAGAGGTGGAGCTGA
AGAAGGGAGCCACTCTCAAGTTCACGCTGGATAATACCTACATGGAAAAGGGTAAGAGAACATCCTGTGGCGGGACTACA
AGAACATCTGCAAGGTGGTGGAAGTGGGCTGCAAGATCTACATGGATGATGGGCTAATTTCTCTCCAAGTGAAGCAGAAG
GATGCTCACTTTCTGGTGACAGAGGTGGAAAATGGTGGCTCCTTGGGCAGCAAGATGGGTGTGAACCTTCCTGGGGCTGC
CGTGGACCTGCCTGCCATGTTGGAGAAGGACATCCAGGACCTGAAGTTTGGGGGCGAGCAATATGTCGATATGATGTTTT
CATCATTCATCTGCAAGACATCTGATGTCCATGAAGTTAGGAAGGTCTTGGGAGAGAAAGGAAAGAACAGCAAGATAACC
AGCAAAATTGAGAATCATGATGGGGGTTGGAGGTTTGATGAAATCCTGGAGGCCAGTGATGGGATTATGGGAGCTCGTGG
TGAT

Alignment

ORF - retro_ptro_2322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.83 %
• Parental protein coverage: 55.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMN
          M.KPHSEA..AFIQTQQLHAAMADTFLEHMC.LD.DSPPITA..TGIICT.GPAS...E.LK..IKSGMN
Retrocopy MLKPHSEARAAFIQTQQLHAAMADTFLEHMCCLDTDSPPITAWSTGIICTMGPASPLLEMLKKTIKSGMN

Parental  VARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATL
          VA.LN.SHG.HEYH.ETIKNVRTATESFASD.ILY.P.AVA.DTKGPEI..G..KGSGTAEVELKKGATL
Retrocopy VAHLN-SHGAHEYHTETIKNVRTATESFASDSILYQPIAVAPDTKGPEIPAGPVKGSGTAEVELKKGATL

Parental  KITLDNAYMEKCD-ENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGV
          K.TLDN.YMEK...ENILW.DYKNICKVVEVG.KIY.DDGLISLQVKQK.A.FLVTEVENGGSLGSK.GV
Retrocopy KFTLDNTYMEKGK<ENILWRDYKNICKVVEVGCKIYMDDGLISLQVKQKDAHFLVTEVENGGSLGSKMGV

Parental  NLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRR
          NLPGAAVDLPA..EKDIQDLKFG.EQ.VDM.F.SFI.K.SDVHEVRKVLGEKGKN.KI.SKIENH.G..R
Retrocopy NLPGAAVDLPAMLEKDIQDLKFGGEQYVDMMFSSFICKTSDVHEVRKVLGEKGKNSKITSKIENHDGGWR

Parental  FDEILEASDGIMVARGD
          FDEILEASDGIM.ARGD
Retrocopy FDEILEASDGIMGARGD

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	0.04 RPM	880.46 RPM
SRP007412_cerebellum	0.07 RPM	977.34 RPM
SRP007412_heart	0.03 RPM	361.03 RPM
SRP007412_kidney	0.08 RPM	355.48 RPM
SRP007412_liver	0.00 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_2322 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2322 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2322 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3418

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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,