RetrogeneDB ID: retro_ptro_130

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:19561714..19562166(+)
• Located in intron of: ENSPTRG00000000269

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS14
• Ensembl ID: ENSPTRG00000017418
• Aliases: None
• Description: ribosomal protein S14 [Source:HGNC Symbol;Acc:10387]

Sequence

>retro_ptro_130
ATGGCACCTGGAAAGGGGAAGGAAAAGAAGGAAGAACAGGTCATCAACCTCGGACCTCAGGTGGCTGAAGGGGAGAATGT
ATTTGGTGTCTGCCATATCTTTGCATCCTTCAATGACACTTTTGTCCATGTCACGGATCTTTCTGGCAAACAAACCATCT
GCCGTGTGACTGGTGGGATGAAGGTGAAGGCAGACCGAGATGAATCCTCGCCATATGCTGCTATGTTGACCACCCAGGAT
GTGGCCCAGAGGTGCAAGGAGCTGGGTATCATTGCCCTACACATCCAACTCCGGGCCACAGGAGGAAATAGGACCAAGAC
CCTTGGACCTGGGGCCCAGTCGGCCCTCAGAGCCCTTGCCTGCTTGGGTATGAAGATCGGGAGGATTGAGGACGTCACCC
CCATCACCTCTGACAGCACTCTCAGGAAGGGGGTTGCCGTGGTCGCCGTCTG

Alignment

ORF - retro_ptro_130 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPRKGKEKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMKVKADRDESS
          MAP.KGKEKKEEQVI.LGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK.TICRVTGGMKVKADRDESS
Retrocopy MAPGKGKEKKEEQVINLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKQTICRVTGGMKVKADRDESS

Parental  PYAAMLAAQDVAQRCKELGITALHIKLRATGGNRTKTPGPGAQSALRALARSGMKIGRIEDVTPIPSDST
          PYAAML..QDVAQRCKELGI.ALHI.LRATGGNRTKT.GPGAQSALRALA..GMKIGRIEDVTPI.SDST
Retrocopy PYAAMLTTQDVAQRCKELGIIALHIQLRATGGNRTKTLGPGAQSALRALACLGMKIGRIEDVTPITSDST

Parental  RRK-GGRRGRRL
          .RK.GG.RGRRL
Retrocopy LRK<GGCRGRRL

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	0.70 RPM	194.37 RPM
SRP007412_cerebellum	1.15 RPM	223.23 RPM
SRP007412_heart	0.29 RPM	179.92 RPM
SRP007412_kidney	1.07 RPM	394.87 RPM
SRP007412_liver	0.65 RPM	302.63 RPM
SRP007412_testis	1.79 RPM	216.77 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_130 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_130 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_130 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_119
Gorilla gorilla	retro_ggor_222
Pongo abelii	retro_pabe_494
Macaca mulatta	retro_mmul_358

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004644	2 retrocopies	retro_amel_1390, retro_amel_524,
Bos taurus	ENSBTAG00000008570	2 retrocopies	retro_btau_1109, retro_btau_213,
Canis familiaris	ENSCAFG00000018094	2 retrocopies	retro_cfam_1589, retro_cfam_301,
Callithrix jacchus	ENSCJAG00000020981	1 retrocopy	retro_cjac_89,
Cavia porcellus	ENSCPOG00000024408	2 retrocopies	retro_cpor_253, retro_cpor_284,
Dipodomys ordii	ENSDORG00000007146	2 retrocopies	retro_dord_174, retro_dord_330,
Gorilla gorilla	ENSGGOG00000024593	8 retrocopies	retro_ggor_1225, retro_ggor_2080, retro_ggor_2135, retro_ggor_2199, retro_ggor_222, retro_ggor_2362, retro_ggor_2548, retro_ggor_316,
Latimeria chalumnae	ENSLACG00000016164	1 retrocopy	retro_lcha_12,
Loxodonta africana	ENSLAFG00000031195	2 retrocopies	retro_lafr_235, retro_lafr_67,
Macropus eugenii	ENSMEUG00000014907	1 retrocopy	retro_meug_619,
Microcebus murinus	ENSMICG00000002900	2 retrocopies	retro_mmur_1569, retro_mmur_433,
Myotis lucifugus	ENSMLUG00000013279	4 retrocopies	retro_mluc_1837, retro_mluc_205, retro_mluc_2464, retro_mluc_2485,
Macaca mulatta	ENSMMUG00000002848	5 retrocopies	retro_mmul_1921, retro_mmul_1983, retro_mmul_358, retro_mmul_570, retro_mmul_90,
Mustela putorius furo	ENSMPUG00000013776	1 retrocopy	retro_mputfur_127,
Nomascus leucogenys	ENSNLEG00000010366	1 retrocopy	retro_nleu_101,
Oryctolagus cuniculus	ENSOCUG00000011509	1 retrocopy	retro_ocun_128,
Otolemur garnettii	ENSOGAG00000000721	1 retrocopy	retro_ogar_286,
Procavia capensis	ENSPCAG00000015960	3 retrocopies	retro_pcap_198, retro_pcap_443, retro_pcap_73,
Pan troglodytes	ENSPTRG00000017418	8 retrocopies	retro_ptro_1086, retro_ptro_130 , retro_ptro_2030, retro_ptro_2104, retro_ptro_2184, retro_ptro_224, retro_ptro_2367, retro_ptro_2570,
Rattus norvegicus	ENSRNOG00000018774	10 retrocopies	retro_rnor_1313, retro_rnor_1467, retro_rnor_1532, retro_rnor_1759, retro_rnor_1875, retro_rnor_1918, retro_rnor_2181, retro_rnor_228, retro_rnor_2728, retro_rnor_873,
Sorex araneus	ENSSARG00000014249	1 retrocopy	retro_sara_537,