RetrogeneDB ID: retro_ptro_2104

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:155650818..155651269(-)
• Located in intron of: None

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_2104
CCTTCCAAGAGGAAGAAGAAAAAGGAAGAACAGGTCATCAGCCTCGGACCTCAGGTGGTTGAAGGAGAGAATGTATTTGG
TGCCTGCCACATCTTTGTCTCCTTCAATGACACCTTTGTCCATGTCACTGATGTTTCTGGCAAGGGAACTACCTGCCATG
TGGCTGCCAGGATGAAGATGAAAGCTGACAGGATGAATCCTCACCACACACTGCCATGTCGGCTGCCCAGGAGGTGGCCC
AGCAGTGCAAGGAGCTGGGGCATTACTGCCCTACACATTTGCAAACTCCAGGCCACAGCAGGAAATAGGACCAAGCACCC
TGGACCTAGGGCCCAGTCGGCCCTCAGAACCCTTGCCTGCTTGGGGATGAAGATCGGGGCAGATCGAGGATGTCACTCCC
ATTCCCCTCCGACAGCACTAGAGGAAGGAGGATTGCCATGGTCACCGCCTG

Alignment

ORF - retro_ptro_2104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.48 %
• Parental protein coverage: 98.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PRKGKEKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMKVKADR-DESSP
          P.K.K.KKEEQVISLGPQV.EGENVFG.CHIF.SFNDTFVHVTD.SGK.T.C.V...MK.KADR.DESSP
Retrocopy PSKRKKKKEEQVISLGPQVVEGENVFGACHIFVSFNDTFVHVTDVSGKGTTCHVAARMKMKADR<DESSP

Parental  YAAMLAAQDVAQRCKEL-GITALHI-KLRATGGNRTKTPGPGAQSALRALARSGMKI-GRIEDVTPI-PS
          ..AM.AAQ.VAQ.CKEL.GITALHI.KL.AT.GNRTK.PGP.AQSALR.LA..GMKI.G.IEDVTPI.PS
Retrocopy HTAMSAAQEVAQQCKEL>GITALHICKLQATAGNRTKHPGPRAQSALRTLACLGMKI>GQIEDVTPI>PS

Parental  DSTR-RKGGRRGRRL
          DSTR.RK....G.RL
Retrocopy DSTR<RKEDCHGHRL

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	194.37 RPM
SRP007412_cerebellum	0.00 RPM	223.23 RPM
SRP007412_heart	0.06 RPM	179.92 RPM
SRP007412_kidney	0.00 RPM	394.87 RPM
SRP007412_liver	0.03 RPM	302.63 RPM
SRP007412_testis	0.11 RPM	216.77 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2104 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2104 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3113
Gorilla gorilla	retro_ggor_2135
Pongo abelii	retro_pabe_2571
Macaca mulatta	retro_mmul_1983

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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,