RetrogeneDB ID: retro_ptro_2404

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:155940675..155941180(+)
• Located in intron of: ENSPTRG00000018724

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL17
• Ensembl ID: ENSPTRG00000010012
• Aliases: None
• Description: ribosomal protein L17 [Source:HGNC Symbol;Acc:10307]

Sequence

>retro_ptro_2404
AGAGGTTCAAATCTTTGTGTTCACTTTAAGAACACCTGTGAAATTCCCTAGGCTATCAAAGGTATGCATATATGAAAAGC
CACCAAGTTATCTGAAAGATGTCACTTTACGGAAACAATGTGTACCATTCCAGCCTTCCAAGGGTGGAGTTGGTAGGTAT
GCACAGGCCAAACAGTGGGGCTGGACACAGGGCTGGTGGCCCAACAAGAATGCTGCATTTTTCCTGCACATGTTTAAAAG
TGCAGAGAGTGATGCTGAATTCAAGGGTTTAGATGTAGATTCTCTGGTCACTAAGCACATCCAGGTGAATGAAACACCCA
AGATGGGCCACTGTACTTTCAGAGCTCATGGTCGGATGAATTTATATATGAGCTCCCTCTGCCACATGGAGATGATCCTC
GCTGGAAAGGAATAAATTGTTCCTAAACCACAAGAGATGGCTGCATGGAAAAAAAAAAAAAAAGTGTCCCATAAGAAACT
GAAGAAACAAAAACTCATGGCACGA

Alignment

ORF - retro_ptro_2404 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.6 %
• Parental protein coverage: 90.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RGSNLRVHFKNTRETAQAIKGMHIRKATK-YLKDVTLQKQCVPFRRYNGGVGRCAQAKQWGWTQGRWPKK
          RGSNL.VHFKNT.E...AIKGMHI.KATK.YLKDVTL.KQCVPF....GGVGR.AQAKQWGWTQG.WP.K
Retrocopy RGSNLCVHFKNTCEIP*AIKGMHI*KATK>YLKDVTLRKQCVPFQPSKGGVGRYAQAKQWGWTQGWWPNK

Parental  SAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILTEKEQI
          .A.F.LHM.K.AES.AE.KGLDVDSLV..HIQVN..PKM...T.RAHGR.N.YMSS.CH.EMIL..KE.I
Retrocopy NAAFFLHMFKSAESDAEFKGLDVDSLVTKHIQVNETPKMGHCTFRAHGRMNLYMSSLCHMEMILAGKE*I

Parental  VPKPEEEVA--QKKKISQKKLKKQKLMAR
          VPKP.E..A.......S.KKLKKQKLMAR
Retrocopy VPKPQEMAAWXXXXXVSHKKLKKQKLMAR

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	0.04 RPM	167.43 RPM
SRP007412_cerebellum	0.04 RPM	232.84 RPM
SRP007412_heart	0.00 RPM	106.24 RPM
SRP007412_kidney	0.08 RPM	275.85 RPM
SRP007412_liver	0.00 RPM	136.70 RPM
SRP007412_testis	0.00 RPM	130.99 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2404 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2404 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2404 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2921

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 229 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,
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,
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,
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,
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,
Pan troglodytes	ENSPTRG00000010012	51 retrocopies	retro_ptro_1069, retro_ptro_1130, retro_ptro_1193, retro_ptro_1215, retro_ptro_1227, retro_ptro_1267, retro_ptro_1271, retro_ptro_1294, retro_ptro_1308, retro_ptro_1350, retro_ptro_1443, retro_ptro_1509, retro_ptro_161, retro_ptro_1634, retro_ptro_1651, retro_ptro_1653, retro_ptro_1682, retro_ptro_1733, retro_ptro_1790, retro_ptro_183, retro_ptro_1887, retro_ptro_1963, retro_ptro_2059, retro_ptro_2267, retro_ptro_2270, retro_ptro_2355, retro_ptro_2392, retro_ptro_2404 , retro_ptro_242, retro_ptro_2450, retro_ptro_2486, retro_ptro_2498, retro_ptro_2515, retro_ptro_2576, retro_ptro_2659, retro_ptro_2675, retro_ptro_2680, retro_ptro_2693, retro_ptro_2706, retro_ptro_2787, retro_ptro_280, retro_ptro_2997, retro_ptro_3073, retro_ptro_490, retro_ptro_509, retro_ptro_523, retro_ptro_719, retro_ptro_793, retro_ptro_948, retro_ptro_973, retro_ptro_985,
Vicugna pacos	ENSVPAG00000009568	1 retrocopy	retro_vpac_10,