RetrogeneDB ID: retro_pabe_3070

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:63376594..63377050(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS18
• Ensembl ID: ENSPPYG00000025953
• Aliases: None
• Description: ribosomal protein S18 [Source:HGNC Symbol;Acc:10401]

Sequence

>retro_pabe_3070
ATGTCTCTAGTGATCCCTGAAAAGTTTCAGCATATTTTGTGAGTACTTGATACCAACATCAATGAGCAGTGGAAAATAGC
CTTTGCCATCACTGCCATTAAAGATGTGGGTTGAAGATATGCTCATGTGGTGTTGAGGAAAGCAGACATTGACTTCACCA
AGAGGGCAGGAGAACTCACTGAGGATAAGGTGGAACGTGTGATCACCATTATGCAGAATCCATGCCAGTTCAAGATCCCA
GACTGGTCCTTGAACAGACAGAATGATGTAAAGGATGGAAAATATAGCCAGGTCCTAGCCAATGTTCTGGACAACAAGCT
CCATGAGGACCTGGAGTGACTGAAGAAGATTCAGGTTCATAGAGGGCTGTGCCACTTCTGGGGCCTTTGTGTCCGAGGCC
AGCACACCAAGACCACTGGCTGCCGTGGCCATACCGTTGGTGTGTCTAAGAAGAAA

Alignment

ORF - retro_pabe_3070 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITI
          MSLVIPEKFQHIL.VL.TNI....KIAFAITAIK.VG.RYAHVVLRKADID.TKRAGELTED.VERVITI
Retrocopy MSLVIPEKFQHIL*VLDTNINEQWKIAFAITAIKDVG*RYAHVVLRKADIDFTKRAGELTEDKVERVITI

Parental  MQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTTG
          MQNP.Q.KIPDW.LNRQ.DVKDGKYSQVLAN.LDNKL.EDLE.LKKI..HRGL.HFWGL.VRGQHTKTTG
Retrocopy MQNPCQFKIPDWSLNRQNDVKDGKYSQVLANVLDNKLHEDLE*LKKIQVHRGLCHFWGLCVRGQHTKTTG

Parental  RRGRTVGVSKKK
          .RG.TVGVSKKK
Retrocopy CRGHTVGVSKKK

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	151.44 RPM
SRP007412_cerebellum	0.00 RPM	115.40 RPM
SRP007412_heart	0.00 RPM	185.68 RPM
SRP007412_kidney	0.00 RPM	391.53 RPM
SRP007412_liver	0.00 RPM	335.61 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3070 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3070 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3070 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_3061

---

Parental genes homology:

Parental genes homology involve 34 parental genes, and 203 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002918	1 retrocopy	retro_acar_206,
Ailuropoda melanoleuca	ENSAMEG00000001623	2 retrocopies	retro_amel_1617, retro_amel_381,
Bos taurus	ENSBTAG00000002648	2 retrocopies	retro_btau_1052, retro_btau_614,
Canis familiaris	ENSCAFG00000000950	7 retrocopies	retro_cfam_1311, retro_cfam_1607, retro_cfam_2132, retro_cfam_414, retro_cfam_522, retro_cfam_789, retro_cfam_856,
Choloepus hoffmanni	ENSCHOG00000003746	5 retrocopies	retro_chof_1248, retro_chof_1727, retro_chof_1768, retro_chof_1968, retro_chof_444,
Callithrix jacchus	ENSCJAG00000021650	5 retrocopies	retro_cjac_22, retro_cjac_245, retro_cjac_2529, retro_cjac_2893, retro_cjac_2955,
Cavia porcellus	ENSCPOG00000019675	4 retrocopies	retro_cpor_1044, retro_cpor_130, retro_cpor_860, retro_cpor_971,
Dasypus novemcinctus	ENSDNOG00000012084	13 retrocopies	retro_dnov_1295, retro_dnov_1398, retro_dnov_1448, retro_dnov_1675, retro_dnov_1770, retro_dnov_2008, retro_dnov_2115, retro_dnov_2223, retro_dnov_2288, retro_dnov_327, retro_dnov_363, retro_dnov_384, retro_dnov_399,
Dipodomys ordii	ENSDORG00000013825	6 retrocopies	retro_dord_185, retro_dord_326, retro_dord_426, retro_dord_481, retro_dord_50, retro_dord_772,
Erinaceus europaeus	ENSEEUG00000010297	8 retrocopies	retro_eeur_201, retro_eeur_261, retro_eeur_380, retro_eeur_460, retro_eeur_473, retro_eeur_498, retro_eeur_667, retro_eeur_689,
Felis catus	ENSFCAG00000004013	7 retrocopies	retro_fcat_1058, retro_fcat_1536, retro_fcat_166, retro_fcat_222, retro_fcat_313, retro_fcat_327, retro_fcat_430,
Homo sapiens	ENSG00000231500	2 retrocopies	retro_hsap_1806, retro_hsap_1974,
Gorilla gorilla	ENSGGOG00000006571	5 retrocopies	retro_ggor_1496, retro_ggor_2310, retro_ggor_344, retro_ggor_77, retro_ggor_93,
Loxodonta africana	ENSLAFG00000032173	1 retrocopy	retro_lafr_1171,
Macropus eugenii	ENSMEUG00000016770	11 retrocopies	retro_meug_1296, retro_meug_1737, retro_meug_1807, retro_meug_1946, retro_meug_212, retro_meug_310, retro_meug_344, retro_meug_387, retro_meug_566, retro_meug_625, retro_meug_627,
Myotis lucifugus	ENSMLUG00000007360	2 retrocopies	retro_mluc_181, retro_mluc_932,
Macaca mulatta	ENSMMUG00000003867	1 retrocopy	retro_mmul_2198,
Monodelphis domestica	ENSMODG00000014210	4 retrocopies	retro_mdom_1041, retro_mdom_1286, retro_mdom_1514, retro_mdom_642,
Mustela putorius furo	ENSMPUG00000002306	6 retrocopies	retro_mputfur_1110, retro_mputfur_1204, retro_mputfur_399, retro_mputfur_687, retro_mputfur_888, retro_mputfur_943,
Mus musculus	ENSMUSG00000008668	2 retrocopies	retro_mmus_57, retro_mmus_66,
Nomascus leucogenys	ENSNLEG00000006840	10 retrocopies	retro_nleu_1074, retro_nleu_1161, retro_nleu_1176, retro_nleu_1466, retro_nleu_219, retro_nleu_2572, retro_nleu_2616, retro_nleu_525, retro_nleu_60, retro_nleu_737,
Oryctolagus cuniculus	ENSOCUG00000010546	1 retrocopy	retro_ocun_31,
Otolemur garnettii	ENSOGAG00000006225	7 retrocopies	retro_ogar_1498, retro_ogar_1832, retro_ogar_2372, retro_ogar_472, retro_ogar_608, retro_ogar_709, retro_ogar_905,
Procavia capensis	ENSPCAG00000005854	2 retrocopies	retro_pcap_235, retro_pcap_319,
Pongo abelii	ENSPPYG00000025953	14 retrocopies	retro_pabe_1138, retro_pabe_128, retro_pabe_1481, retro_pabe_1482, retro_pabe_1813, retro_pabe_1881, retro_pabe_2303, retro_pabe_2407, retro_pabe_2663, retro_pabe_2833, retro_pabe_2967, retro_pabe_3013, retro_pabe_3070 , retro_pabe_368,
Pan troglodytes	ENSPTRG00000018039	1 retrocopy	retro_ptro_121,
Pteropus vampyrus	ENSPVAG00000001902	6 retrocopies	retro_pvam_295, retro_pvam_556, retro_pvam_691, retro_pvam_708, retro_pvam_829, retro_pvam_875,
Rattus norvegicus	ENSRNOG00000028505	4 retrocopies	retro_rnor_102, retro_rnor_234, retro_rnor_29, retro_rnor_70,
Sarcophilus harrisii	ENSSHAG00000006857	2 retrocopies	retro_shar_265, retro_shar_563,
Sarcophilus harrisii	ENSSHAG00000008658	1 retrocopy	retro_shar_618,
Sus scrofa	ENSSSCG00000001502	5 retrocopies	retro_sscr_112, retro_sscr_156, retro_sscr_157, retro_sscr_2, retro_sscr_831,
Ictidomys tridecemlineatus	ENSSTOG00000002417	13 retrocopies	retro_itri_1023, retro_itri_1049, retro_itri_1121, retro_itri_1316, retro_itri_1484, retro_itri_228, retro_itri_397, retro_itri_547, retro_itri_690, retro_itri_742, retro_itri_854, retro_itri_875, retro_itri_878,
Tupaia belangeri	ENSTBEG00000012708	40 retrocopies	retro_tbel_1070, retro_tbel_1739, retro_tbel_1745, retro_tbel_1806, retro_tbel_1818, retro_tbel_1827, retro_tbel_1855, retro_tbel_205, retro_tbel_2087, retro_tbel_211, retro_tbel_2299, retro_tbel_2309, retro_tbel_2312, retro_tbel_234, retro_tbel_2364, retro_tbel_2424, retro_tbel_2473, retro_tbel_250, retro_tbel_2682, retro_tbel_2768, retro_tbel_295, retro_tbel_3189, retro_tbel_3317, retro_tbel_3383, retro_tbel_3625, retro_tbel_363, retro_tbel_3686, retro_tbel_3731, retro_tbel_3870, retro_tbel_4100, retro_tbel_4215, retro_tbel_4365, retro_tbel_45, retro_tbel_4562, retro_tbel_4578, retro_tbel_462, retro_tbel_57, retro_tbel_578, retro_tbel_856, retro_tbel_941,
Tursiops truncatus	ENSTTRG00000004302	3 retrocopies	retro_ttru_1012, retro_ttru_1553, retro_ttru_837,