RetrogeneDB ID: retro_ptro_540

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:39168817..39169147(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL18
• Ensembl ID: ENSPTRG00000011245
• Aliases: None
• Description: ribosomal protein L18 [Source:HGNC Symbol;Acc:10310]

Sequence

>retro_ptro_540
ATAGGAGCTGACATCCTCCACAACAAGGACCGAAAGGTTCCCTGCAAGGAGCCCAAGAGCCCGGATACCTACCTGAGGCT
GTTGGTCAAGCTGTACAGGTTTCTGGCCAGACGAACCAACTCCACATTCAACCAGGTTGTGCTGAAGAGGTTGTTTATGA
GTCGCACCAAGGGGCCACCTCTGTCCCCTTTCCGGATAATCCGCAAAATGAAGCTTCCTGGCCGGGTAAAGAAAACCGCC
GTGCTTGTGGGGACTGTAAGGGATGATGTGCGGGTACAGGAGGTGCCCAAACTGAAGGTTTGTGCGCTGCGCATGACCAG
CCGGGCCCGC

Alignment

ORF - retro_ptro_540 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.64 %
• Parental protein coverage: 58.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGVDIRHNKDRKVRRKEPKSQDIYLRLLVKLYRFLARRTNSTFNQVVLKRLFMSRTNRPPLSLSRMIRKM
          .G.DI.HNKDRKV..KEPKS.D.YLRLLVKLYRFLARRTNSTFNQVVLKRLFMSRT..PPLS..R.IRKM
Retrocopy IGADILHNKDRKVPCKEPKSPDTYLRLLVKLYRFLARRTNSTFNQVVLKRLFMSRTKGPPLSPFRIIRKM

Parental  KLPGRENKTAVVVGTITDDVRVQEVPKLKVCALRVTSRAR
          KLPGR..KTAV.VGT..DDVRVQEVPKLKVCALR.TSRAR
Retrocopy KLPGRVKKTAVLVGTVRDDVRVQEVPKLKVCALRMTSRAR

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	158.15 RPM
SRP007412_cerebellum	0.00 RPM	183.22 RPM
SRP007412_heart	0.00 RPM	72.87 RPM
SRP007412_kidney	0.00 RPM	327.63 RPM
SRP007412_liver	0.00 RPM	344.95 RPM
SRP007412_testis	0.53 RPM	20.55 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_540 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_540 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_540 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_772

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 94 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009140	6 retrocopies	retro_chof_1408, retro_chof_1668, retro_chof_1697, retro_chof_2025, retro_chof_427, retro_chof_436,
Callithrix jacchus	ENSCJAG00000000377	4 retrocopies	retro_cjac_1659, retro_cjac_2114, retro_cjac_2296, retro_cjac_529,
Felis catus	ENSFCAG00000008652	4 retrocopies	retro_fcat_1055, retro_fcat_1268, retro_fcat_1596, retro_fcat_718,
Gorilla gorilla	ENSGGOG00000024878	7 retrocopies	retro_ggor_1038, retro_ggor_1280, retro_ggor_2200, retro_ggor_2550, retro_ggor_2624, retro_ggor_847, retro_ggor_937,
Macropus eugenii	ENSMEUG00000000640	1 retrocopy	retro_meug_1568,
Macaca mulatta	ENSMMUG00000022158	3 retrocopies	retro_mmul_32, retro_mmul_55, retro_mmul_92,
Monodelphis domestica	ENSMODG00000014099	1 retrocopy	retro_mdom_906,
Mustela putorius furo	ENSMPUG00000003891	4 retrocopies	retro_mputfur_135, retro_mputfur_1410, retro_mputfur_529, retro_mputfur_974,
Nomascus leucogenys	ENSNLEG00000004537	11 retrocopies	retro_nleu_1124, retro_nleu_1136, retro_nleu_1410, retro_nleu_1799, retro_nleu_2006, retro_nleu_2380, retro_nleu_2464, retro_nleu_2597, retro_nleu_547, retro_nleu_577, retro_nleu_976,
Otolemur garnettii	ENSOGAG00000003562	16 retrocopies	retro_ogar_1167, retro_ogar_1474, retro_ogar_1563, retro_ogar_1753, retro_ogar_1978, retro_ogar_2394, retro_ogar_2419, retro_ogar_2527, retro_ogar_2613, retro_ogar_2833, retro_ogar_3319, retro_ogar_3456, retro_ogar_3458, retro_ogar_3459, retro_ogar_492, retro_ogar_996,
Oreochromis niloticus	ENSONIG00000006539	1 retrocopy	retro_onil_43,
Pan troglodytes	ENSPTRG00000011245	10 retrocopies	retro_ptro_1084, retro_ptro_1155, retro_ptro_2187, retro_ptro_2574, retro_ptro_2649, retro_ptro_2790, retro_ptro_540 , retro_ptro_730, retro_ptro_822, retro_ptro_908,
Rattus norvegicus	ENSRNOG00000021035	14 retrocopies	retro_rnor_1068, retro_rnor_1072, retro_rnor_1154, retro_rnor_1186, retro_rnor_1337, retro_rnor_1359, retro_rnor_2174, retro_rnor_2224, retro_rnor_2847, retro_rnor_2890, retro_rnor_516, retro_rnor_685, retro_rnor_856, retro_rnor_857,
Sarcophilus harrisii	ENSSHAG00000006564	2 retrocopies	retro_shar_571, retro_shar_659,
Sus scrofa	ENSSSCG00000025928	5 retrocopies	retro_sscr_1028, retro_sscr_118, retro_sscr_836, retro_sscr_864, retro_sscr_925,
Ictidomys tridecemlineatus	ENSSTOG00000012258	5 retrocopies	retro_itri_261, retro_itri_323, retro_itri_828, retro_itri_853, retro_itri_957,