RetrogeneDB ID: retro_ptro_1039

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:23397809..23398237(-)
• Located in intron of: ENSPTRG00000030355

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS18C
• Ensembl ID: ENSPTRG00000016233
• Aliases: None
• Description: mitochondrial ribosomal protein S18C [Source:HGNC Symbol;Acc:16633]

Sequence

>retro_ptro_1039
ATGGCCACTATAGTTGCTCTTTGCAGTGGTCTGGGGAGGAAGAAGTTGACACACCTTGTAATGGCTGCTGTTAGCCTTAC
ACATCCCAGGACTCATATGGTGCTATGGAGAAGAGGTTGTTCACAATATAAACAGATATCCAGCAATGAGGACCTGCCCA
TTCCAATGGAAAATTCTTATAAAGAAGCCCTTAAGAAATGTATCTTGTGTGGAAAGCAGGTAGATTTTAAGAATGTACAG
TGTCCCAGTTTATTTCTCCATTTGTTGGATGCATTTGTGGAAGGCACAAAACAGGTCTTTGTGGGAAGAAACAGAAAGAA
ATCACAAAAGCAATTAAGAGAGCTCAAATAATGGGGTTTCTGCCAGTTACATCCAAGGATGCTGCATATCTCAAGGACCC
TAAAGTTTGTAACATCAGATGTCAGGAG

Alignment

ORF - retro_ptro_1039 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.34 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAVVAVCGGLGRKKLTHLVTAAVSLTHPGTHTVLWRRGCSQ--QVSSNEDLPISMENPYKEPLKKCILC
          MA..VA.C.GLGRKKLTHLV.AAVSLTHP.TH.VLWRRGCSQ..Q.SSNEDLPI.MEN.YKE.LKKCILC
Retrocopy MATIVALCSGLGRKKLTHLVMAAVSLTHPRTHMVLWRRGCSQYKQISSNEDLPIPMENSYKEALKKCILC

Parental  GKHVDYKNVQLLSQFVSPFTGCIYGRHITGLCGKKQK-EITKAIKRAQIMGFMPVTYKDPAYLKDPKVCN
          GK.VD.KNVQ..S.F.........G.......G...K.EITKAIKRAQIMGF.PVT.KD.AYLKDPKVCN
Retrocopy GKQVDFKNVQCPSLFLHLLDAFVEGTKQV-FVGRNRK<EITKAIKRAQIMGFLPVTSKDAAYLKDPKVCN

Parental  IRYRE
          IR..E
Retrocopy IRCQE

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	0.00 RPM	7.35 RPM
SRP007412_cerebellum	0.00 RPM	6.13 RPM
SRP007412_heart	0.00 RPM	9.91 RPM
SRP007412_kidney	0.00 RPM	10.46 RPM
SRP007412_liver	0.00 RPM	9.39 RPM
SRP007412_testis	0.00 RPM	7.38 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1039 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1039 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1039 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1540
Gorilla gorilla	retro_ggor_1173
Pongo abelii	retro_pabe_1276
Macaca mulatta	retro_mmul_2203

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018155	3 retrocopies	retro_btau_1386, retro_btau_309, retro_btau_502,
Callithrix jacchus	ENSCJAG00000005286	3 retrocopies	retro_cjac_1419, retro_cjac_234, retro_cjac_3970,
Cavia porcellus	ENSCPOG00000009198	1 retrocopy	retro_cpor_178,
Dasypus novemcinctus	ENSDNOG00000018326	2 retrocopies	retro_dnov_1030, retro_dnov_152,
Homo sapiens	ENSG00000163319	5 retrocopies	retro_hsap_1540, retro_hsap_2597, retro_hsap_4019, retro_hsap_4684, retro_hsap_969,
Gorilla gorilla	ENSGGOG00000008603	2 retrocopies	retro_ggor_1173, retro_ggor_2908,
Macropus eugenii	ENSMEUG00000010972	2 retrocopies	retro_meug_104, retro_meug_1113,
Myotis lucifugus	ENSMLUG00000017057	1 retrocopy	retro_mluc_2360,
Mus musculus	ENSMUSG00000016833	2 retrocopies	retro_mmus_1546, retro_mmus_2127,
Nomascus leucogenys	ENSNLEG00000009119	4 retrocopies	retro_nleu_111, retro_nleu_1614, retro_nleu_2722, retro_nleu_3010,
Ochotona princeps	ENSOPRG00000004113	2 retrocopies	retro_opri_1041, retro_opri_966,
Pongo abelii	ENSPPYG00000025867	2 retrocopies	retro_pabe_1276, retro_pabe_70,
Pan troglodytes	ENSPTRG00000016233	3 retrocopies	retro_ptro_1039 , retro_ptro_1521, retro_ptro_3113,
Pteropus vampyrus	ENSPVAG00000006439	2 retrocopies	retro_pvam_1326, retro_pvam_1412,
Rattus norvegicus	ENSRNOG00000002178	3 retrocopies	retro_rnor_2264, retro_rnor_2265, retro_rnor_477,
Sarcophilus harrisii	ENSSHAG00000007084	1 retrocopy	retro_shar_718,
Ictidomys tridecemlineatus	ENSSTOG00000007989	1 retrocopy	retro_itri_1231,
Tupaia belangeri	ENSTBEG00000012505	3 retrocopies	retro_tbel_1755, retro_tbel_4724, retro_tbel_508,
Tarsius syrichta	ENSTSYG00000012924	1 retrocopy	retro_tsyr_649,
Tursiops truncatus	ENSTTRG00000004897	2 retrocopies	retro_ttru_144, retro_ttru_1721,