RetrogeneDB ID: retro_cpor_1322

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_7:46045400..46045956(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL18
• Ensembl ID: ENSCPOG00000026334
• Aliases: None
• Description: 60S ribosomal protein L18 [Source:UniProtKB/TrEMBL;Acc:H0W177]

Sequence

>retro_cpor_1322
GGAGTCGACATCTGCTATAACAAGGACCAAAAGGTCCTGCACAAGGAGCCCCAGATCCAGGATATCTACCTGAGGCTGTT
GGTCAAGCTGTACAGGTTTCTGGCCCAACAAACAAACTCCGCCTTCAACCAGGCGGTGCTGAAGAGGTTGTTCATGAGTG
GCACCAACTGAGCACCCCTCTCCCTTTCCTGGGTGATCTGGGAGATGAAGCCTCCTGGTCGGGAAAACAAGACAGCAGTG
GTTGTGGAGGTGTCAGACGACATGCAGGTTCTGGAGGTGTCCAAGCTGAAGGTTTGTATCCTAGGTGTGACCAGCCAGGC
CCACAGTGCATCCTCAAGGCCAGGGGTAAGATACTCACTTTTGACCAGCTGGCCCTGGATTCCCGCAATGGCCATAGCAC
AGTCCTGCTCTCTGGTCCGCATAAGGACCAAGAGATGTGCAGACATTTCAGCAAGGCCCCAGGAGCCCGCACAGCCATAC
CAAACCCTACCTCTGCTCCAAGGTCCAGGAGCTGGACTGTACCAGAAGCAGATGGGCCAGCAGAGCCTACAAGAAC

Alignment

ORF - retro_cpor_1322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.84 %
• Parental protein coverage: 99.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GVDIRHNKDRKVRRKEPKSQDIYLRLLVKLYRFLARRTNSTFNQVVLKRLFMSRTNRPPLSLSRMIRKMK
          GVDI..NKD.KV..KEP..QDIYLRLLVKLYRFLA..TNS.FNQ.VLKRLFMS.TN..PLSLS..I..MK
Retrocopy GVDICYNKDQKVLHKEPQIQDIYLRLLVKLYRFLAQQTNSAFNQAVLKRLFMSGTN*APLSLSWVIWEMK

Parental  LPGRENKTAVVVGTVTDDVRVLEVPKLKVCALRVTSRARSR-ILKAGGKILTFDQLALESPKGRGTVLLS
          .PGRENKTAVVV..V.DD..VLEV.KLKVC.L.VTS.A.S..ILKA.GKILTFDQLAL.S..G..TVLLS
Retrocopy PPGRENKTAVVV-EVSDDMQVLEVSKLKVCILGVTSQAHSA<ILKARGKILTFDQLALDSRNGHSTVLLS

Parental  GPRKGREVYRHFGKAPG-TPHSHTKPYVRSKGRKFERARGRRASRGYKN
          GP.K..E..RHF.KAPG..PHSHTKPY..SK.......R.R.ASR.YKN
Retrocopy GPHKDQEMCRHFSKAPG<SPHSHTKPYLCSKVQELDCTRSRWASRAYKN

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
SRP017611_brain	0.00 RPM	83.57 RPM
SRP017611_kidney	0.00 RPM	155.88 RPM
SRP017611_liver	0.00 RPM	85.88 RPM
SRP040447_lung	0.00 RPM	269.03 RPM
SRP040447_skeletal_muscle	0.00 RPM	210.02 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1322 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1322 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 98 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014872	3 retrocopies	retro_amel_1718, retro_amel_640, retro_amel_740,
Cavia porcellus	ENSCPOG00000026334	4 retrocopies	retro_cpor_1062, retro_cpor_1322 , retro_cpor_703, retro_cpor_733,
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,
Mus musculus	ENSMUSG00000059070	11 retrocopies	retro_mmus_1655, retro_mmus_2025, retro_mmus_2091, retro_mmus_2303, retro_mmus_2462, retro_mmus_2622, retro_mmus_2790, retro_mmus_3424, retro_mmus_3621, retro_mmus_726, retro_mmus_740,
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,
Pongo abelii	ENSPPYG00000010206	6 retrocopies	retro_pabe_1003, retro_pabe_1337, retro_pabe_1402, retro_pabe_2681, retro_pabe_3100, retro_pabe_3176,
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,