RetrogeneDB ID: retro_ptro_2139

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:34182243..34182498(+)
• Located in intron of: ENSPTRG00000024170

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS12
• Ensembl ID: ENSPTRG00000018618
• Aliases: None
• Description: Pan troglodytes ribosomal protein S12 (RPS12), mRNA. [Source:RefSeq mRNA;Acc:NM_001252509]

Sequence

>retro_ptro_2139
CATCTTTGTGTGCCTGCATCCAATTCTGATGAGCCTATGTATGTCAAGTTGGTCAAGGCCCTTTGTGCTGAACACCAAAT
CAACCTAATTAAGGTTGATGACAAGAAACTAGGGGAATGAGTAGGCGACCTCTGTAAAATTGACAGAGAGGGGAAACCCT
GTAAAGTGGTTGGTTGCAGTTGTGTAGTAGTTAAGGACTATGGCAAGGAGTCTCAGCCCAAGGATGTCATCAAAGAGTAC
TTCAAATGCAAGAAA

Alignment

ORF - retro_ptro_2139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.53 %
• Parental protein coverage: 64.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HLCVLASNCDEPMYVKLVEALCAEHQINLIKVDDNKKLGEWVG-LCKIDREGKPRKVVGCSCVVVKDYGK
          HLCV.ASN.DEPMYVKLV.ALCAEHQINLIKVDD.KKLGE.VG.LCKIDREGKP.KVVGCSCVVVKDYGK
Retrocopy HLCVPASNSDEPMYVKLVKALCAEHQINLIKVDD-KKLGE*VGDLCKIDREGKPCKVVGCSCVVVKDYGK

Parental  ESQAKDVIEEYFKCKK
          ESQ.KDVI.EYFKCKK
Retrocopy ESQPKDVIKEYFKCKK

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	0.05 RPM	180.07 RPM
SRP007412_cerebellum	0.07 RPM	84.75 RPM
SRP007412_heart	0.03 RPM	79.60 RPM
SRP007412_kidney	0.21 RPM	293.11 RPM
SRP007412_liver	0.03 RPM	168.52 RPM
SRP007412_testis	0.11 RPM	63.12 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2139 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2139 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2139 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3347
Gorilla gorilla	retro_ggor_1287
Pongo abelii	retro_pabe_2757

---

Parental genes homology:

Parental genes homology involve 28 parental genes, and 271 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010479	1 retrocopy	retro_acar_102,
Ailuropoda melanoleuca	ENSAMEG00000008015	2 retrocopies	retro_amel_79, retro_amel_92,
Bos taurus	ENSBTAG00000001360	7 retrocopies	retro_btau_106, retro_btau_1097, retro_btau_1306, retro_btau_1495, retro_btau_1514, retro_btau_1630, retro_btau_1802,
Callithrix jacchus	ENSCJAG00000002865	34 retrocopies	retro_cjac_1038, retro_cjac_1044, retro_cjac_1205, retro_cjac_1291, retro_cjac_1528, retro_cjac_1602, retro_cjac_1778, retro_cjac_1994, retro_cjac_2039, retro_cjac_2058, retro_cjac_2065, retro_cjac_2101, retro_cjac_2112, retro_cjac_2155, retro_cjac_2337, retro_cjac_2406, retro_cjac_2421, retro_cjac_2461, retro_cjac_2681, retro_cjac_2694, retro_cjac_2858, retro_cjac_301, retro_cjac_3310, retro_cjac_4149, retro_cjac_427, retro_cjac_466, retro_cjac_494, retro_cjac_592, retro_cjac_773, retro_cjac_805, retro_cjac_806, retro_cjac_807, retro_cjac_836, retro_cjac_977,
Cavia porcellus	ENSCPOG00000000429	4 retrocopies	retro_cpor_1096, retro_cpor_304, retro_cpor_32, retro_cpor_380,
Dasypus novemcinctus	ENSDNOG00000006214	31 retrocopies	retro_dnov_1006, retro_dnov_1116, retro_dnov_1262, retro_dnov_1455, retro_dnov_1456, retro_dnov_1642, retro_dnov_1644, retro_dnov_1797, retro_dnov_1879, retro_dnov_1939, retro_dnov_1999, retro_dnov_2112, retro_dnov_2120, retro_dnov_2263, retro_dnov_2312, retro_dnov_2440, retro_dnov_2446, retro_dnov_2472, retro_dnov_2481, retro_dnov_2486, retro_dnov_2517, retro_dnov_2584, retro_dnov_2645, retro_dnov_328, retro_dnov_391, retro_dnov_427, retro_dnov_562, retro_dnov_57, retro_dnov_659, retro_dnov_700, retro_dnov_963,
Equus caballus	ENSECAG00000001599	8 retrocopies	retro_ecab_1012, retro_ecab_1131, retro_ecab_133, retro_ecab_744, retro_ecab_80, retro_ecab_828, retro_ecab_875, retro_ecab_959,
Echinops telfairi	ENSETEG00000006854	14 retrocopies	retro_etel_1129, retro_etel_1512, retro_etel_1580, retro_etel_2016, retro_etel_205, retro_etel_2082, retro_etel_2099, retro_etel_2169, retro_etel_26, retro_etel_280, retro_etel_29, retro_etel_55, retro_etel_578, retro_etel_915,
Felis catus	ENSFCAG00000028402	7 retrocopies	retro_fcat_1084, retro_fcat_1314, retro_fcat_1446, retro_fcat_1880, retro_fcat_537, retro_fcat_664, retro_fcat_796,
Gorilla gorilla	ENSGGOG00000012234	22 retrocopies	retro_ggor_1164, retro_ggor_1287, retro_ggor_1322, retro_ggor_139, retro_ggor_1426, retro_ggor_1441, retro_ggor_1686, retro_ggor_1861, retro_ggor_1894, retro_ggor_2115, retro_ggor_2241, retro_ggor_2261, retro_ggor_2339, retro_ggor_2456, retro_ggor_2489, retro_ggor_2680, retro_ggor_3076, retro_ggor_530, retro_ggor_595, retro_ggor_673, retro_ggor_724, retro_ggor_971,
Gadus morhua	ENSGMOG00000019455	1 retrocopy	retro_gmor_11,
Loxodonta africana	ENSLAFG00000007933	11 retrocopies	retro_lafr_1172, retro_lafr_154, retro_lafr_281, retro_lafr_429, retro_lafr_447, retro_lafr_494, retro_lafr_552, retro_lafr_653, retro_lafr_736, retro_lafr_807, retro_lafr_949,
Microcebus murinus	ENSMICG00000005252	5 retrocopies	retro_mmur_1260, retro_mmur_1527, retro_mmur_391, retro_mmur_491, retro_mmur_98,
Myotis lucifugus	ENSMLUG00000001137	5 retrocopies	retro_mluc_1479, retro_mluc_1552, retro_mluc_1987, retro_mluc_1988, retro_mluc_582,
Macaca mulatta	ENSMMUG00000013237	1 retrocopy	retro_mmul_12,
Mustela putorius furo	ENSMPUG00000014771	1 retrocopy	retro_mputfur_6,
Mus musculus	ENSMUSG00000061983	1 retrocopy	retro_mmus_36,
Nomascus leucogenys	ENSNLEG00000014611	4 retrocopies	retro_nleu_2717, retro_nleu_543, retro_nleu_588, retro_nleu_86,
Oryctolagus cuniculus	ENSOCUG00000001606	14 retrocopies	retro_ocun_1025, retro_ocun_1152, retro_ocun_1271, retro_ocun_1314, retro_ocun_1707, retro_ocun_1875, retro_ocun_1948, retro_ocun_434, retro_ocun_484, retro_ocun_577, retro_ocun_590, retro_ocun_764, retro_ocun_878, retro_ocun_998,
Otolemur garnettii	ENSOGAG00000001309	20 retrocopies	retro_ogar_1173, retro_ogar_1390, retro_ogar_2079, retro_ogar_2082, retro_ogar_2242, retro_ogar_2255, retro_ogar_2417, retro_ogar_2632, retro_ogar_2761, retro_ogar_297, retro_ogar_298, retro_ogar_3173, retro_ogar_3290, retro_ogar_3476, retro_ogar_432, retro_ogar_708, retro_ogar_754, retro_ogar_832, retro_ogar_909, retro_ogar_950,
Pelodiscus sinensis	ENSPSIG00000003457	1 retrocopy	retro_psin_52,
Pan troglodytes	ENSPTRG00000018618	25 retrocopies	retro_ptro_1031, retro_ptro_1203, retro_ptro_1221, retro_ptro_1222, retro_ptro_1310, retro_ptro_1330, retro_ptro_1592, retro_ptro_1604, retro_ptro_1797, retro_ptro_1839, retro_ptro_1995, retro_ptro_2077, retro_ptro_2139 , retro_ptro_2197, retro_ptro_2328, retro_ptro_2350, retro_ptro_2465, retro_ptro_2495, retro_ptro_2711, retro_ptro_2807, retro_ptro_2943, retro_ptro_480, retro_ptro_503, retro_ptro_618, retro_ptro_854,
Pteropus vampyrus	ENSPVAG00000017201	12 retrocopies	retro_pvam_1081, retro_pvam_1291, retro_pvam_164, retro_pvam_258, retro_pvam_260, retro_pvam_265, retro_pvam_271, retro_pvam_316, retro_pvam_553, retro_pvam_657, retro_pvam_818, retro_pvam_884,
Rattus norvegicus	ENSRNOG00000016411	5 retrocopies	retro_rnor_177, retro_rnor_186, retro_rnor_241, retro_rnor_295, retro_rnor_300,
Sorex araneus	ENSSARG00000003170	2 retrocopies	retro_sara_356, retro_sara_8,
Sarcophilus harrisii	ENSSHAG00000008905	6 retrocopies	retro_shar_187, retro_shar_226, retro_shar_475, retro_shar_492, retro_shar_621, retro_shar_671,
Tarsius syrichta	ENSTSYG00000010097	24 retrocopies	retro_tsyr_1010, retro_tsyr_102, retro_tsyr_1123, retro_tsyr_1188, retro_tsyr_129, retro_tsyr_1313, retro_tsyr_1345, retro_tsyr_1398, retro_tsyr_1486, retro_tsyr_1668, retro_tsyr_1955, retro_tsyr_1993, retro_tsyr_205, retro_tsyr_249, retro_tsyr_303, retro_tsyr_419, retro_tsyr_453, retro_tsyr_556, retro_tsyr_645, retro_tsyr_733, retro_tsyr_764, retro_tsyr_801, retro_tsyr_970, retro_tsyr_99,
Vicugna pacos	ENSVPAG00000011504	3 retrocopies	retro_vpac_133, retro_vpac_267, retro_vpac_339,