RetrogeneDB ID: retro_pabe_2800

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:173945933..173946520(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL19
• Ensembl ID: ENSPPYG00000008492
• Aliases: None
• Description: 60S ribosomal protein L19 [Source:UniProtKB/Swiss-Prot;Acc:Q5RB99]

Sequence

>retro_pabe_2800
ATGAGTATGTTCGGGCTTCAGAAGAGGCCCGCTGCTAGTGTCCTCTGCTGTGGCAAGAAGAAGGTCTGGTTGGACCCCAA
TGAGGCCAGTGAAATTGCCAATGCCAACTCCCGTCAGCAGATCTGGGAGCTGATCAAAGATGGGCTGATTATCTGTAAGC
CTGTGACTGTCCATTCCCAGGCTCAATGCCGGAAAAACACCTTGGCCCACCGGAAGGGCAGGCACATGGGTACGGGTAAG
CGAAAGGGTACAGCCAATGCCCCAATGCCAGAGAAGGTCACGTGGTGAGGAGAATGAGGATTCTGCACCCACTGCTCAGA
AGATACCGTGAATCTAAGAAGATCAATTGCCACATGTATCACAGCCTGTACCTGAAGGTGAAGGGGAATATGTTCAAAGA
CAAGCGGATTCTCATGGAACACATCCACAAGCTGAAGGCAGACAAAGCCTGCAAGAAGCTCCTGGCTGACCAGGCTGAGG
CCCGCAGGCCTAAGACCAAGGAAGCACGAAAGCAACGTGAAGAGTGCCTCCAGGCCAAGAAGGAGGGGATCATCAAGACT
TTGTCCAAGGACGAAGAGATGAAGAAA

Alignment

ORF - retro_pabe_2800 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKNTLAR
          MSM..LQKR.A.SVL.CGKKKVWLDPNE..EIANANSRQQI..LIKDGLII.KPVTVHS.A.CRKNTLA.
Retrocopy MSMFGLQKRPAASVLCCGKKKVWLDPNEASEIANANSRQQIWELIKDGLIICKPVTVHSQAQCRKNTLAH

Parental  RKGRHMGIGKRKGTANARMPEKVTW-MRRMRILRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILM
          RKGRHMG.GKRKGTANA.MPEKVTW..RRMRIL..LLRRYRESKKI..HMYHSLYLKVKGN.FK.KRILM
Retrocopy RKGRHMGTGKRKGTANAPMPEKVTW<VRRMRILHPLLRRYRESKKINCHMYHSLYLKVKGNMFKDKRILM

Parental  EHIHKLKADKARKKLLADQAEARRSKTKEARKRREERLQAKKEEIIKTLSKEEETKK
          EHIHKLKADKA.KKLLADQAEARR.KTKEARK.REE.LQAKKE.IIKTLSK.EE.KK
Retrocopy EHIHKLKADKACKKLLADQAEARRPKTKEARKQREECLQAKKEGIIKTLSKDEEMKK

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	99.36 RPM
SRP007412_cerebellum	0.00 RPM	98.38 RPM
SRP007412_heart	0.00 RPM	118.85 RPM
SRP007412_kidney	0.00 RPM	308.13 RPM
SRP007412_liver	0.03 RPM	250.14 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2800 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2800 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2800 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3401
Pan troglodytes	retro_ptro_2311

---

Parental genes homology:

Parental genes homology involve 30 parental genes, and 300 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004121	5 retrocopies	retro_amel_1195, retro_amel_1663, retro_amel_451, retro_amel_531, retro_amel_889,
Bos taurus	ENSBTAG00000002060	5 retrocopies	retro_btau_1241, retro_btau_1254, retro_btau_1371, retro_btau_1480, retro_btau_761,
Canis familiaris	ENSCAFG00000016493	14 retrocopies	retro_cfam_1011, retro_cfam_1647, retro_cfam_1767, retro_cfam_1799, retro_cfam_1892, retro_cfam_2082, retro_cfam_2129, retro_cfam_328, retro_cfam_357, retro_cfam_486, retro_cfam_851, retro_cfam_909, retro_cfam_932, retro_cfam_940,
Choloepus hoffmanni	ENSCHOG00000006023	7 retrocopies	retro_chof_1041, retro_chof_1065, retro_chof_1135, retro_chof_1930, retro_chof_2567, retro_chof_338, retro_chof_993,
Callithrix jacchus	ENSCJAG00000008520	4 retrocopies	retro_cjac_131, retro_cjac_220, retro_cjac_32, retro_cjac_64,
Dasypus novemcinctus	ENSDNOG00000019742	7 retrocopies	retro_dnov_1478, retro_dnov_1897, retro_dnov_2, retro_dnov_2170, retro_dnov_2431, retro_dnov_691, retro_dnov_720,
Dipodomys ordii	ENSDORG00000004330	1 retrocopy	retro_dord_105,
Equus caballus	ENSECAG00000025080	6 retrocopies	retro_ecab_104, retro_ecab_319, retro_ecab_351, retro_ecab_456, retro_ecab_497, retro_ecab_905,
Homo sapiens	ENSG00000108298	21 retrocopies	retro_hsap_1085, retro_hsap_1802, retro_hsap_2072, retro_hsap_2157, retro_hsap_2209, retro_hsap_2406, retro_hsap_2651, retro_hsap_2679, retro_hsap_2850, retro_hsap_3012, retro_hsap_3155, retro_hsap_3274, retro_hsap_3401, retro_hsap_3885, retro_hsap_3933, retro_hsap_399, retro_hsap_3991, retro_hsap_4219, retro_hsap_4680, retro_hsap_4774, retro_hsap_739,
Loxodonta africana	ENSLAFG00000018257	3 retrocopies	retro_lafr_1045, retro_lafr_479, retro_lafr_88,
Macropus eugenii	ENSMEUG00000013900	10 retrocopies	retro_meug_1047, retro_meug_1201, retro_meug_1226, retro_meug_1256, retro_meug_1262, retro_meug_1486, retro_meug_1878, retro_meug_2108, retro_meug_2155, retro_meug_82,
Microcebus murinus	ENSMICG00000002663	5 retrocopies	retro_mmur_1213, retro_mmur_231, retro_mmur_469, retro_mmur_520, retro_mmur_678,
Myotis lucifugus	ENSMLUG00000012555	11 retrocopies	retro_mluc_1149, retro_mluc_1473, retro_mluc_1694, retro_mluc_2032, retro_mluc_2034, retro_mluc_2398, retro_mluc_2400, retro_mluc_2616, retro_mluc_573, retro_mluc_887, retro_mluc_890,
Macaca mulatta	ENSMMUG00000004235	2 retrocopies	retro_mmul_283, retro_mmul_63,
Monodelphis domestica	ENSMODG00000012693	2 retrocopies	retro_mdom_53, retro_mdom_750,
Mustela putorius furo	ENSMPUG00000015041	5 retrocopies	retro_mputfur_1221, retro_mputfur_1248, retro_mputfur_1479, retro_mputfur_357, retro_mputfur_688,
Mus musculus	ENSMUSG00000017404	25 retrocopies	retro_mmus_1174, retro_mmus_1235, retro_mmus_1248, retro_mmus_1273, retro_mmus_1323, retro_mmus_1397, retro_mmus_1591, retro_mmus_1614, retro_mmus_1699, retro_mmus_1700, retro_mmus_1877, retro_mmus_1885, retro_mmus_1964, retro_mmus_2301, retro_mmus_2688, retro_mmus_2749, retro_mmus_2967, retro_mmus_3110, retro_mmus_3187, retro_mmus_3310, retro_mmus_341, retro_mmus_3413, retro_mmus_507, retro_mmus_571, retro_mmus_600,
Nomascus leucogenys	ENSNLEG00000000748	19 retrocopies	retro_nleu_1182, retro_nleu_1570, retro_nleu_1602, retro_nleu_1620, retro_nleu_1889, retro_nleu_2171, retro_nleu_2236, retro_nleu_2284, retro_nleu_2335, retro_nleu_2430, retro_nleu_2446, retro_nleu_2538, retro_nleu_2695, retro_nleu_2702, retro_nleu_2735, retro_nleu_3116, retro_nleu_479, retro_nleu_540, retro_nleu_656,
Ochotona princeps	ENSOPRG00000007092	2 retrocopies	retro_opri_1220, retro_opri_987,
Procavia capensis	ENSPCAG00000015228	1 retrocopy	retro_pcap_141,
Pongo abelii	ENSPPYG00000008492	20 retrocopies	retro_pabe_1546, retro_pabe_1687, retro_pabe_1709, retro_pabe_1815, retro_pabe_2177, retro_pabe_2300, retro_pabe_2320, retro_pabe_2496, retro_pabe_2625, retro_pabe_2799, retro_pabe_2800 , retro_pabe_3166, retro_pabe_3278, retro_pabe_3299, retro_pabe_3513, retro_pabe_3635, retro_pabe_3829, retro_pabe_4, retro_pabe_973, retro_pabe_980,
Pan troglodytes	ENSPTRG00000009086	22 retrocopies	retro_ptro_1180, retro_ptro_1385, retro_ptro_1642, retro_ptro_1676, retro_ptro_1786, retro_ptro_1806, retro_ptro_1930, retro_ptro_2036, retro_ptro_2214, retro_ptro_2279, retro_ptro_2311, retro_ptro_2645, retro_ptro_2709, retro_ptro_2865, retro_ptro_2998, retro_ptro_305, retro_ptro_3109, retro_ptro_3179, retro_ptro_467, retro_ptro_525, retro_ptro_673, retro_ptro_737,
Pteropus vampyrus	ENSPVAG00000008498	9 retrocopies	retro_pvam_1191, retro_pvam_1332, retro_pvam_183, retro_pvam_244, retro_pvam_468, retro_pvam_792, retro_pvam_914, retro_pvam_918, retro_pvam_950,
Rattus norvegicus	ENSRNOG00000004741	37 retrocopies	retro_rnor_1029, retro_rnor_1039, retro_rnor_1295, retro_rnor_1338, retro_rnor_1405, retro_rnor_1440, retro_rnor_1449, retro_rnor_1478, retro_rnor_1512, retro_rnor_1525, retro_rnor_1558, retro_rnor_1577, retro_rnor_1765, retro_rnor_1766, retro_rnor_1795, retro_rnor_1814, retro_rnor_1860, retro_rnor_1885, retro_rnor_1905, retro_rnor_1907, retro_rnor_1970, retro_rnor_1981, retro_rnor_208, retro_rnor_2169, retro_rnor_2522, retro_rnor_2536, retro_rnor_2708, retro_rnor_2773, retro_rnor_2783, retro_rnor_2921, retro_rnor_2943, retro_rnor_326, retro_rnor_426, retro_rnor_434, retro_rnor_464, retro_rnor_465, retro_rnor_829,
Sarcophilus harrisii	ENSSHAG00000016482	4 retrocopies	retro_shar_159, retro_shar_287, retro_shar_317, retro_shar_415,
Sus scrofa	ENSSSCG00000017509	3 retrocopies	retro_sscr_1108, retro_sscr_398, retro_sscr_913,
Ictidomys tridecemlineatus	ENSSTOG00000011120	5 retrocopies	retro_itri_1174, retro_itri_1180, retro_itri_1330, retro_itri_178, retro_itri_200,
Tupaia belangeri	ENSTBEG00000008077	31 retrocopies	retro_tbel_1024, retro_tbel_1150, retro_tbel_1200, retro_tbel_1248, retro_tbel_1507, retro_tbel_1620, retro_tbel_173, retro_tbel_1752, retro_tbel_1791, retro_tbel_1826, retro_tbel_1942, retro_tbel_199, retro_tbel_2166, retro_tbel_2529, retro_tbel_2558, retro_tbel_2687, retro_tbel_2751, retro_tbel_2855, retro_tbel_3256, retro_tbel_3347, retro_tbel_3493, retro_tbel_3758, retro_tbel_4501, retro_tbel_4606, retro_tbel_4631, retro_tbel_759, retro_tbel_799, retro_tbel_835, retro_tbel_867, retro_tbel_957, retro_tbel_988,
Tarsius syrichta	ENSTSYG00000008698	10 retrocopies	retro_tsyr_1164, retro_tsyr_1267, retro_tsyr_1310, retro_tsyr_1330, retro_tsyr_1770, retro_tsyr_1916, retro_tsyr_540, retro_tsyr_713, retro_tsyr_782, retro_tsyr_93,
Tursiops truncatus	ENSTTRG00000006687	4 retrocopies	retro_ttru_1131, retro_ttru_1132, retro_ttru_1389, retro_ttru_1804,