RetrogeneDB ID: retro_hsap_3620

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:81083734..81084286(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000219547
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL17
• Ensembl ID: ENSG00000265681
• Aliases: RPL17, L17, PD-1, RPL23
• Description: ribosomal protein L17 [Source:HGNC Symbol;Acc:10307]

Sequence

>retro_hsap_3620
ATGGTGCCCTATACACTTGACCGGGAGAACCCCACAAAATCATGCAAATCAAGAGGTTCCAATCTTTGTATTCACCTTAA
GAACACTCGTGAAACTGCCCAGGCCATCAAGGGTATGCATATATGAAAAGCCACAAAATATCTGAAAGATGTCACTTTAC
AGAAACGGTGCGTACCATTCCGACGTTACAATGGTGGAGTTGGCAGGTGTGCCCAGGCCAAGCAGTGGGGCTAGACACAA
GGTTGGTGGCCCAAAAAGAGTGCTGAATTTTTGCTGCACATGCTTAAAAATGCAGACAGTAATGGTGAACTTAAGGGTTT
AGATGTAGACTCTCTGGCCATTGAGCATATCCAAATGAATAAAGCATCTAAGATGTGCTGCCAGACCTACAGAGCTCATA
GTCGGATTAACCCATACATGAGCTCTCCCTGCCACATTGAGATGAGCCTTACTGAAAAGGAACAGATTGCTCCTAAACCA
GAAGAAGAAGTTGCCCAGAAGAAAAAGATATCCCAGAAGAAACTGATGAAACAAAAACTTATGGCATGGGAG

Alignment

ORF - retro_hsap_3620 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLQKQCVPFRRYNGGVGRC
          MV.Y.LD.ENPTKSCKSRGSNL..H.KNTRETAQAIKGMHI.KATKYLKDVTLQK.CVPFRRYNGGVGRC
Retrocopy MVPYTLDRENPTKSCKSRGSNLCIHLKNTRETAQAIKGMHI*KATKYLKDVTLQKRCVPFRRYNGGVGRC

Parental  AQAKQWGWTQGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYM
          AQAKQWG.TQG.WPKKSAEFLLHMLKNA.SN.ELKGLDVDSL.IEHIQ.NKA.KM...TYRAH.RINPYM
Retrocopy AQAKQWG*TQGWWPKKSAEFLLHMLKNADSNGELKGLDVDSLAIEHIQMNKASKMCCQTYRAHSRINPYM

Parental  SSPCHIEMILTEKEQIVPKPEEEVAQKKKISQKKLKKQKLMARE
          SSPCHIEM.LTEKEQI.PK...............L.KQKLMA.E
Retrocopy SSPCHIEMSLTEKEQIAPKXXXXXXXXXXXXXXXLMKQKLMAWE

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
bodymap2_adipose	0.00 RPM	20.32 RPM
bodymap2_adrenal	0.04 RPM	36.44 RPM
bodymap2_brain	0.02 RPM	15.35 RPM
bodymap2_breast	0.00 RPM	17.82 RPM
bodymap2_colon	0.02 RPM	33.37 RPM
bodymap2_heart	0.02 RPM	5.98 RPM
bodymap2_kidney	0.00 RPM	9.80 RPM
bodymap2_liver	0.00 RPM	5.87 RPM
bodymap2_lung	0.00 RPM	25.18 RPM
bodymap2_lymph_node	0.00 RPM	29.64 RPM
bodymap2_ovary	0.06 RPM	60.36 RPM
bodymap2_prostate	0.00 RPM	25.53 RPM
bodymap2_skeletal_muscle	0.00 RPM	3.95 RPM
bodymap2_testis	0.00 RPM	20.53 RPM
bodymap2_thyroid	0.00 RPM	52.37 RPM
bodymap2_white_blood_cells	0.00 RPM	10.40 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3620 was not detected

EST

No EST(s) were mapped for retro_hsap_3620 retrocopy.

TSS

No TSS is located nearby retro_hsap_3620 retrocopy 5' end.

Lab

retro_hsap_3620 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3620 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 415 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009498	40 retrocopies	retro_amel_1147, retro_amel_1150, retro_amel_1252, retro_amel_1273, retro_amel_132, retro_amel_1422, retro_amel_1435, retro_amel_1487, retro_amel_1541, retro_amel_156, retro_amel_1567, retro_amel_1582, retro_amel_1599, retro_amel_1622, retro_amel_1624, retro_amel_1652, retro_amel_1703, retro_amel_1704, retro_amel_1743, retro_amel_1757, retro_amel_184, retro_amel_1908, retro_amel_1922, retro_amel_208, retro_amel_359, retro_amel_401, retro_amel_425, retro_amel_426, retro_amel_452, retro_amel_486, retro_amel_589, retro_amel_731, retro_amel_736, retro_amel_780, retro_amel_820, retro_amel_834, retro_amel_865, retro_amel_950, retro_amel_953, retro_amel_980,
Canis familiaris	ENSCAFG00000019044	7 retrocopies	retro_cfam_102, retro_cfam_171, retro_cfam_175, retro_cfam_189, retro_cfam_2, retro_cfam_239, retro_cfam_34,
Choloepus hoffmanni	ENSCHOG00000007872	50 retrocopies	retro_chof_1020, retro_chof_1021, retro_chof_107, retro_chof_1232, retro_chof_130, retro_chof_137, retro_chof_1405, retro_chof_1432, retro_chof_1448, retro_chof_1453, retro_chof_1471, retro_chof_1475, retro_chof_153, retro_chof_1634, retro_chof_1671, retro_chof_1678, retro_chof_1754, retro_chof_1786, retro_chof_187, retro_chof_1871, retro_chof_1895, retro_chof_1901, retro_chof_1908, retro_chof_2038, retro_chof_204, retro_chof_2133, retro_chof_2140, retro_chof_221, retro_chof_2243, retro_chof_2415, retro_chof_2458, retro_chof_246, retro_chof_2489, retro_chof_2534, retro_chof_2570, retro_chof_2610, retro_chof_2640, retro_chof_463, retro_chof_507, retro_chof_564, retro_chof_65, retro_chof_690, retro_chof_716, retro_chof_759, retro_chof_775, retro_chof_798, retro_chof_875, retro_chof_899, retro_chof_945, retro_chof_953,
Callithrix jacchus	ENSCJAG00000004779	4 retrocopies	retro_cjac_122, retro_cjac_248, retro_cjac_360, retro_cjac_376,
Echinops telfairi	ENSETEG00000011322	10 retrocopies	retro_etel_1787, retro_etel_1810, retro_etel_1900, retro_etel_1936, retro_etel_1954, retro_etel_207, retro_etel_396, retro_etel_470, retro_etel_565, retro_etel_831,
Homo sapiens	ENSG00000215472	1 retrocopy	retro_hsap_2367,
Homo sapiens	ENSG00000265681	33 retrocopies	retro_hsap_1158, retro_hsap_1382, retro_hsap_1423, retro_hsap_1448, retro_hsap_1590, retro_hsap_172, retro_hsap_1728, retro_hsap_1751, retro_hsap_1783, retro_hsap_181, retro_hsap_1893, retro_hsap_1938, retro_hsap_202, retro_hsap_2149, retro_hsap_2398, retro_hsap_2457, retro_hsap_2491, retro_hsap_2582, retro_hsap_2786, retro_hsap_2905, retro_hsap_2933, retro_hsap_295, retro_hsap_3176, retro_hsap_3475, retro_hsap_356, retro_hsap_3620 , retro_hsap_3798, retro_hsap_3932, retro_hsap_3943, retro_hsap_3967, retro_hsap_3988, retro_hsap_714, retro_hsap_735,
Gorilla gorilla	ENSGGOG00000026697	1 retrocopy	retro_ggor_167,
Latimeria chalumnae	ENSLACG00000008835	1 retrocopy	retro_lcha_38,
Loxodonta africana	ENSLAFG00000005569	16 retrocopies	retro_lafr_1001, retro_lafr_1036, retro_lafr_1060, retro_lafr_1130, retro_lafr_177, retro_lafr_186, retro_lafr_207, retro_lafr_213, retro_lafr_256, retro_lafr_293, retro_lafr_354, retro_lafr_721, retro_lafr_731, retro_lafr_773, retro_lafr_860, retro_lafr_933,
Macropus eugenii	ENSMEUG00000016709	26 retrocopies	retro_meug_1111, retro_meug_127, retro_meug_1285, retro_meug_1485, retro_meug_1821, retro_meug_188, retro_meug_1886, retro_meug_191, retro_meug_204, retro_meug_2159, retro_meug_2167, retro_meug_2183, retro_meug_257, retro_meug_326, retro_meug_355, retro_meug_373, retro_meug_410, retro_meug_413, retro_meug_509, retro_meug_58, retro_meug_703, retro_meug_738, retro_meug_740, retro_meug_779, retro_meug_81, retro_meug_934,
Microcebus murinus	ENSMICG00000017102	14 retrocopies	retro_mmur_1046, retro_mmur_1047, retro_mmur_107, retro_mmur_1305, retro_mmur_1360, retro_mmur_1614, retro_mmur_195, retro_mmur_325, retro_mmur_335, retro_mmur_427, retro_mmur_484, retro_mmur_754, retro_mmur_817, retro_mmur_855,
Macaca mulatta	ENSMMUG00000018837	26 retrocopies	retro_mmul_1015, retro_mmul_1046, retro_mmul_1205, retro_mmul_1216, retro_mmul_1225, retro_mmul_1441, retro_mmul_163, retro_mmul_172, retro_mmul_1784, retro_mmul_1858, retro_mmul_1952, retro_mmul_2006, retro_mmul_2008, retro_mmul_2257, retro_mmul_2268, retro_mmul_2284, retro_mmul_2304, retro_mmul_2512, retro_mmul_46, retro_mmul_474, retro_mmul_589, retro_mmul_652, retro_mmul_669, retro_mmul_825, retro_mmul_956, retro_mmul_971,
Mustela putorius furo	ENSMPUG00000000801	7 retrocopies	retro_mputfur_1008, retro_mputfur_126, retro_mputfur_1349, retro_mputfur_16, retro_mputfur_184, retro_mputfur_40, retro_mputfur_536,
Procavia capensis	ENSPCAG00000003103	8 retrocopies	retro_pcap_193, retro_pcap_196, retro_pcap_197, retro_pcap_200, retro_pcap_206, retro_pcap_250, retro_pcap_363, retro_pcap_52,
Pongo abelii	ENSPPYG00000009151	43 retrocopies	retro_pabe_1177, retro_pabe_1178, retro_pabe_1179, retro_pabe_1197, retro_pabe_1373, retro_pabe_1408, retro_pabe_1448, retro_pabe_1464, retro_pabe_1531, retro_pabe_1565, retro_pabe_1574, retro_pabe_1725, retro_pabe_1807, retro_pabe_1832, retro_pabe_1902, retro_pabe_2052, retro_pabe_2053, retro_pabe_2088, retro_pabe_2102, retro_pabe_2164, retro_pabe_2231, retro_pabe_2317, retro_pabe_2520, retro_pabe_2635, retro_pabe_2638, retro_pabe_2871, retro_pabe_2917, retro_pabe_2921, retro_pabe_2971, retro_pabe_3020, retro_pabe_3029, retro_pabe_3103, retro_pabe_3187, retro_pabe_3248, retro_pabe_3253, retro_pabe_3262, retro_pabe_3277, retro_pabe_347, retro_pabe_3493, retro_pabe_539, retro_pabe_567, retro_pabe_617, retro_pabe_882,
Pteropus vampyrus	ENSPVAG00000001969	76 retrocopies	retro_pvam_1003, retro_pvam_1005, retro_pvam_1020, retro_pvam_1036, retro_pvam_1037, retro_pvam_104, retro_pvam_1042, retro_pvam_1085, retro_pvam_1093, retro_pvam_1105, retro_pvam_1155, retro_pvam_1162, retro_pvam_1186, retro_pvam_1194, retro_pvam_1204, retro_pvam_1218, retro_pvam_1279, retro_pvam_1336, retro_pvam_1338, retro_pvam_1351, retro_pvam_1366, retro_pvam_1372, retro_pvam_138, retro_pvam_1392, retro_pvam_1397, retro_pvam_1407, retro_pvam_1409, retro_pvam_142, retro_pvam_143, retro_pvam_1452, retro_pvam_1454, retro_pvam_182, retro_pvam_206, retro_pvam_220, retro_pvam_263, retro_pvam_268, retro_pvam_278, retro_pvam_292, retro_pvam_309, retro_pvam_339, retro_pvam_348, retro_pvam_395, retro_pvam_40, retro_pvam_402, retro_pvam_417, retro_pvam_424, retro_pvam_439, retro_pvam_442, retro_pvam_455, retro_pvam_464, retro_pvam_497, retro_pvam_520, retro_pvam_55, retro_pvam_571, retro_pvam_577, retro_pvam_584, retro_pvam_588, retro_pvam_596, retro_pvam_604, retro_pvam_608, retro_pvam_654, retro_pvam_659, retro_pvam_684, retro_pvam_700, retro_pvam_701, retro_pvam_705, retro_pvam_712, retro_pvam_716, retro_pvam_726, retro_pvam_751, retro_pvam_756, retro_pvam_777, retro_pvam_862, retro_pvam_88, retro_pvam_925, retro_pvam_966,
Tarsius syrichta	ENSTSYG00000007402	20 retrocopies	retro_tsyr_1042, retro_tsyr_1298, retro_tsyr_1349, retro_tsyr_1416, retro_tsyr_1555, retro_tsyr_159, retro_tsyr_180, retro_tsyr_1801, retro_tsyr_1940, retro_tsyr_2021, retro_tsyr_2053, retro_tsyr_2088, retro_tsyr_253, retro_tsyr_304, retro_tsyr_693, retro_tsyr_752, retro_tsyr_77, retro_tsyr_819, retro_tsyr_860, retro_tsyr_868,
Tursiops truncatus	ENSTTRG00000005797	31 retrocopies	retro_ttru_1153, retro_ttru_1338, retro_ttru_1374, retro_ttru_1436, retro_ttru_1509, retro_ttru_1716, retro_ttru_1757, retro_ttru_178, retro_ttru_1784, retro_ttru_1811, retro_ttru_1854, retro_ttru_1856, retro_ttru_193, retro_ttru_1932, retro_ttru_232, retro_ttru_264, retro_ttru_299, retro_ttru_447, retro_ttru_49, retro_ttru_568, retro_ttru_609, retro_ttru_627, retro_ttru_636, retro_ttru_660, retro_ttru_691, retro_ttru_703, retro_ttru_747, retro_ttru_800, retro_ttru_836, retro_ttru_884, retro_ttru_992,
Vicugna pacos	ENSVPAG00000009568	1 retrocopy	retro_vpac_10,