RetrogeneDB ID: retro_ptro_30

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 16:76859550..76860177(+)
• Located in intron of: ENSPTRG00000008372

Retrocopy information

• Ensembl ID: ENSPTRG00000039478
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPS8
• Ensembl ID: ENSPTRG00000000659
• Aliases: None
• Description: ribosomal protein S8 [Source:HGNC Symbol;Acc:10441]

Sequence

>retro_ptro_30
ATGGGCATCTCTCGGGACAACTGGCACAAGCGCCGCAAAACCGGGGGCAAGAGAAAGCCCTACCACAAGAAGCGGAAGTA
TGAGTTGGGGCGCCCAGCTGCCAACACCAAGATTGGCCCCCGCCGCATCCACACAGTCCGTGTGCGGGGAGGTAACAAGA
AATACCGTGCCCTGAGGTTGGACGTGGGGAATTTCTCCTGGGGCTCAGAGTGTTGTACTCGTAAAACAAGGATCATCGAT
GTTGTCTACAATGCATCTAATAATGAGCTGGTTCGTACCAAGACCCTGGTGAAGAATTGCATCGTGCTCATCGACAGCAC
ACCGTACCGACAGTGGTACGAGTCCCACTATGCGCTGCCCCTGGGCCGCAAGAAGGGAGCCAAGCTGACTCCTGAGGAAG
AAGAGATTTTAAACAAAAAACGATCTAAAAAAATTCAGAAGAAATATGATGAAAGGAAAAAGAATGCCAAAATCAGCAGT
CTCCTGGAGGAGCAGTTCCAGCAGGGCAAGCTTCTTGCGTGCATCGCTTCAAGGCCGGGACAGTGTGGCCGAGCAGATGG
CTATGTGCTAGAGGGCAAAGAGTTGGAGTTCTATCTTAGGAAAATCAAGGCCCGCAAAGGCAAATAA

Alignment

ORF - retro_ptro_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLDVGNFSWGSE
          MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLDVGNFSWGSE
Retrocopy MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLDVGNFSWGSE

Parental  CCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNKK
          CCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNKK
Retrocopy CCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNKK

Parental  RSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRKIKARKGK
          RSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRKIKARKGK
Retrocopy RSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRKIKARKGK

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	2.70 RPM	133.93 RPM
SRP007412_cerebellum	0.14 RPM	91.45 RPM
SRP007412_heart	0.15 RPM	64.24 RPM
SRP007412_kidney	0.21 RPM	147.13 RPM
SRP007412_liver	0.29 RPM	116.99 RPM
SRP007412_testis	0.21 RPM	20.34 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_30 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_30 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_30 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 165 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015697	1 retrocopy	retro_acar_124,
Ailuropoda melanoleuca	ENSAMEG00000014147	3 retrocopies	retro_amel_1883, retro_amel_373, retro_amel_972,
Bos taurus	ENSBTAG00000015285	2 retrocopies	retro_btau_1388, retro_btau_1593,
Canis familiaris	ENSCAFG00000004745	8 retrocopies	retro_cfam_1336, retro_cfam_1662, retro_cfam_1730, retro_cfam_2139, retro_cfam_2177, retro_cfam_261, retro_cfam_589, retro_cfam_791,
Choloepus hoffmanni	ENSCHOG00000008785	10 retrocopies	retro_chof_1197, retro_chof_1258, retro_chof_1466, retro_chof_1638, retro_chof_2066, retro_chof_2617, retro_chof_2633, retro_chof_274, retro_chof_331, retro_chof_951,
Callithrix jacchus	ENSCJAG00000004197	5 retrocopies	retro_cjac_1068, retro_cjac_181, retro_cjac_3138, retro_cjac_6, retro_cjac_951,
Cavia porcellus	ENSCPOG00000000723	3 retrocopies	retro_cpor_1099, retro_cpor_335, retro_cpor_621,
Dasypus novemcinctus	ENSDNOG00000025236	3 retrocopies	retro_dnov_1717, retro_dnov_802, retro_dnov_908,
Dipodomys ordii	ENSDORG00000009287	1 retrocopy	retro_dord_429,
Homo sapiens	ENSG00000142937	8 retrocopies	retro_hsap_1467, retro_hsap_1536, retro_hsap_1942, retro_hsap_2034, retro_hsap_2791, retro_hsap_3158, retro_hsap_3410, retro_hsap_635,
Gorilla gorilla	ENSGGOG00000005645	5 retrocopies	retro_ggor_1127, retro_ggor_1170, retro_ggor_1357, retro_ggor_1465, retro_ggor_556,
Macropus eugenii	ENSMEUG00000001388	1 retrocopy	retro_meug_119,
Microcebus murinus	ENSMICG00000008024	4 retrocopies	retro_mmur_1180, retro_mmur_1434, retro_mmur_1501, retro_mmur_380,
Myotis lucifugus	ENSMLUG00000001559	30 retrocopies	retro_mluc_1114, retro_mluc_1132, retro_mluc_1165, retro_mluc_1277, retro_mluc_1288, retro_mluc_1418, retro_mluc_1467, retro_mluc_1476, retro_mluc_1486, retro_mluc_1634, retro_mluc_1656, retro_mluc_1689, retro_mluc_1808, retro_mluc_1911, retro_mluc_1938, retro_mluc_2043, retro_mluc_2055, retro_mluc_2085, retro_mluc_2111, retro_mluc_2153, retro_mluc_2182, retro_mluc_2209, retro_mluc_2414, retro_mluc_460, retro_mluc_662, retro_mluc_730, retro_mluc_773, retro_mluc_820, retro_mluc_821, retro_mluc_906,
Macaca mulatta	ENSMMUG00000015270	2 retrocopies	retro_mmul_275, retro_mmul_70,
Monodelphis domestica	ENSMODG00000028389	1 retrocopy	retro_mdom_998,
Mustela putorius furo	ENSMPUG00000013485	6 retrocopies	retro_mputfur_334, retro_mputfur_337, retro_mputfur_493, retro_mputfur_780, retro_mputfur_908, retro_mputfur_986,
Oryctolagus cuniculus	ENSOCUG00000012476	1 retrocopy	retro_ocun_168,
Otolemur garnettii	ENSOGAG00000006922	16 retrocopies	retro_ogar_1156, retro_ogar_1746, retro_ogar_1895, retro_ogar_2501, retro_ogar_2529, retro_ogar_2556, retro_ogar_2699, retro_ogar_2723, retro_ogar_2947, retro_ogar_308, retro_ogar_3291, retro_ogar_3436, retro_ogar_394, retro_ogar_521, retro_ogar_730, retro_ogar_805,
Pan troglodytes	ENSPTRG00000000659	1 retrocopy	retro_ptro_30 ,
Pteropus vampyrus	ENSPVAG00000009859	10 retrocopies	retro_pvam_1285, retro_pvam_1315, retro_pvam_1345, retro_pvam_403, retro_pvam_419, retro_pvam_463, retro_pvam_514, retro_pvam_578, retro_pvam_685, retro_pvam_991,
Rattus norvegicus	ENSRNOG00000018768	2 retrocopies	retro_rnor_222, retro_rnor_235,
Sorex araneus	ENSSARG00000000899	1 retrocopy	retro_sara_462,
Sarcophilus harrisii	ENSSHAG00000000111	5 retrocopies	retro_shar_408, retro_shar_472, retro_shar_480, retro_shar_636, retro_shar_667,
Sus scrofa	ENSSSCG00000003930	4 retrocopies	retro_sscr_353, retro_sscr_550, retro_sscr_607, retro_sscr_919,
Ictidomys tridecemlineatus	ENSSTOG00000006322	3 retrocopies	retro_itri_1337, retro_itri_1380, retro_itri_750,
Tupaia belangeri	ENSTBEG00000000418	20 retrocopies	retro_tbel_1066, retro_tbel_1537, retro_tbel_1538, retro_tbel_163, retro_tbel_1699, retro_tbel_2356, retro_tbel_244, retro_tbel_2580, retro_tbel_3058, retro_tbel_3230, retro_tbel_3478, retro_tbel_3905, retro_tbel_3950, retro_tbel_4241, retro_tbel_4250, retro_tbel_4530, retro_tbel_552, retro_tbel_803, retro_tbel_827, retro_tbel_934,
Tarsius syrichta	ENSTSYG00000005525	5 retrocopies	retro_tsyr_1412, retro_tsyr_1507, retro_tsyr_2176, retro_tsyr_552, retro_tsyr_734,
Tursiops truncatus	ENSTTRG00000003388	4 retrocopies	retro_ttru_1839, retro_ttru_282, retro_ttru_300, retro_ttru_344,