RetrogeneDB ID: retro_cpor_1408

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_8:51822702..51823087(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000022096
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS16
• Ensembl ID: ENSCPOG00000011359
• Aliases: None
• Description: None

Sequence

>retro_cpor_1408
AGCACAGCCATGGCACACTGCAAACGGGGCAATAGCCTCATCAAGGTGAACGGGCGTCCCCTGGAGGTGATCAAGCCGCA
CATGCTACAGTATAAGTTACTGGAGCCTGTTCTGCTTCTGGGCAAGGAGCGGTTTGCTGGTGTTGACATCCGTGTCCGTG
TGAAGGGTGGTGGGCATGTGGCTCAGATTTACCCTATCCGGCAGTCTATCTCCAAAGCCCTGATGGCGTATTACCAGAAA
TATGTGGATGAGGCTTCCCAAGAAAGAGATCAAAGATGTTCTCATCCAGTATGACCGGACCCTGCTGGTAGCTGAACCCT
GCTGCTGCGAATCCAAAAAGTTTGGAGGCCCTGGTGCCCATGCTCGTTAGCAGAAATCCTACCGA

Alignment

ORF - retro_cpor_1408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.6 %
• Parental protein coverage: 85.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGKERFAGVDIRVRVKGGGHVAQIYAIRQSI
          .TA.AHCKRGN.LIKVNGRPLE.I.P..LQYKLLEPVLLLGKERFAGVDIRVRVKGGGHVAQIY.IRQSI
Retrocopy STAMAHCKRGNSLIKVNGRPLEVIKPHMLQYKLLEPVLLLGKERFAGVDIRVRVKGGGHVAQIYPIRQSI

Parental  SKALVAYYQKYVDEAS-KKEIKDILIQYDRTLLVADPRRCESKKFGGPGARARYQKSYR
          SKAL.AYYQKYVDEAS.KKEIKD.LIQYDRTLLVA.P..CESKKFGGPGA.AR.QKSYR
Retrocopy SKALMAYYQKYVDEAS>KKEIKDVLIQYDRTLLVAEPCCCESKKFGGPGAHAR*QKSYR

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	98.64 RPM
SRP017611_kidney	0.00 RPM	208.33 RPM
SRP017611_liver	0.04 RPM	117.17 RPM
SRP040447_lung	0.05 RPM	278.59 RPM
SRP040447_skeletal_muscle	0.05 RPM	371.03 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1408 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1408 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 33 parental genes, and 149 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014176	1 retrocopy	retro_acar_194,
Ailuropoda melanoleuca	ENSAMEG00000008470	8 retrocopies	retro_amel_1105, retro_amel_1143, retro_amel_1463, retro_amel_1790, retro_amel_1865, retro_amel_306, retro_amel_668, retro_amel_840,
Bos taurus	ENSBTAG00000021093	3 retrocopies	retro_btau_1509, retro_btau_167, retro_btau_441,
Canis familiaris	ENSCAFG00000005501	6 retrocopies	retro_cfam_1349, retro_cfam_1754, retro_cfam_2142, retro_cfam_2147, retro_cfam_799, retro_cfam_908,
Callithrix jacchus	ENSCJAG00000014170	6 retrocopies	retro_cjac_2641, retro_cjac_2737, retro_cjac_3019, retro_cjac_885, retro_cjac_905, retro_cjac_949,
Cavia porcellus	ENSCPOG00000011359	3 retrocopies	retro_cpor_1266, retro_cpor_1408 , retro_cpor_1515,
Dasypus novemcinctus	ENSDNOG00000001527	3 retrocopies	retro_dnov_2260, retro_dnov_2315, retro_dnov_308,
Equus caballus	ENSECAG00000004311	2 retrocopies	retro_ecab_186, retro_ecab_779,
Echinops telfairi	ENSETEG00000015290	4 retrocopies	retro_etel_1825, retro_etel_1834, retro_etel_193, retro_etel_351,
Felis catus	ENSFCAG00000010743	4 retrocopies	retro_fcat_1258, retro_fcat_1709, retro_fcat_1806, retro_fcat_1976,
Homo sapiens	ENSG00000105193	11 retrocopies	retro_hsap_118, retro_hsap_1658, retro_hsap_1736, retro_hsap_1977, retro_hsap_2064, retro_hsap_2230, retro_hsap_2327, retro_hsap_3593, retro_hsap_4209, retro_hsap_787, retro_hsap_813,
Gorilla gorilla	ENSGGOG00000014414	10 retrocopies	retro_ggor_110, retro_ggor_1250, retro_ggor_1344, retro_ggor_1664, retro_ggor_1766, retro_ggor_193, retro_ggor_2423, retro_ggor_2819, retro_ggor_652, retro_ggor_667,
Loxodonta africana	ENSLAFG00000001541	1 retrocopy	retro_lafr_1191,
Macropus eugenii	ENSMEUG00000010380	2 retrocopies	retro_meug_1306, retro_meug_612,
Microcebus murinus	ENSMICG00000006110	4 retrocopies	retro_mmur_1006, retro_mmur_1058, retro_mmur_375, retro_mmur_798,
Myotis lucifugus	ENSMLUG00000029089	5 retrocopies	retro_mluc_1906, retro_mluc_2096, retro_mluc_2174, retro_mluc_2529, retro_mluc_481,
Macaca mulatta	ENSMMUG00000019370	8 retrocopies	retro_mmul_1018, retro_mmul_1080, retro_mmul_1175, retro_mmul_1219, retro_mmul_1403, retro_mmul_20, retro_mmul_767, retro_mmul_862,
Monodelphis domestica	ENSMODG00000013545	4 retrocopies	retro_mdom_1668, retro_mdom_1823, retro_mdom_815, retro_mdom_856,
Mustela putorius furo	ENSMPUG00000017722	5 retrocopies	retro_mputfur_283, retro_mputfur_322, retro_mputfur_447, retro_mputfur_701, retro_mputfur_985,
Mus musculus	ENSMUSG00000037563	11 retrocopies	retro_mmus_1780, retro_mmus_2058, retro_mmus_2125, retro_mmus_2697, retro_mmus_2727, retro_mmus_3091, retro_mmus_3173, retro_mmus_3198, retro_mmus_3202, retro_mmus_700, retro_mmus_771,
Nomascus leucogenys	ENSNLEG00000014388	3 retrocopies	retro_nleu_1266, retro_nleu_248, retro_nleu_46,
Oryctolagus cuniculus	ENSOCUG00000002150	14 retrocopies	retro_ocun_1028, retro_ocun_1073, retro_ocun_1394, retro_ocun_1430, retro_ocun_1436, retro_ocun_1774, retro_ocun_371, retro_ocun_580, retro_ocun_632, retro_ocun_645, retro_ocun_670, retro_ocun_837, retro_ocun_906, retro_ocun_986,
Otolemur garnettii	ENSOGAG00000004497	4 retrocopies	retro_ogar_1229, retro_ogar_1309, retro_ogar_1313, retro_ogar_98,
Oreochromis niloticus	ENSONIG00000000006	1 retrocopy	retro_onil_52,
Pelodiscus sinensis	ENSPSIG00000016930	1 retrocopy	retro_psin_55,
Pan troglodytes	ENSPTRG00000010970	11 retrocopies	retro_ptro_1223, retro_ptro_1318, retro_ptro_1376, retro_ptro_1577, retro_ptro_1699, retro_ptro_2432, retro_ptro_2857, retro_ptro_2953, retro_ptro_2957, retro_ptro_548, retro_ptro_565,
Rattus norvegicus	ENSRNOG00000019578	3 retrocopies	retro_rnor_10, retro_rnor_1823, retro_rnor_302,
Sorex araneus	ENSSARG00000000852	1 retrocopy	retro_sara_595,
Sus scrofa	ENSSSCG00000010712	1 retrocopy	retro_sscr_731,
Sus scrofa	ENSSSCG00000020817	3 retrocopies	retro_sscr_478, retro_sscr_5, retro_sscr_723,
Ictidomys tridecemlineatus	ENSSTOG00000006794	1 retrocopy	retro_itri_321,
Tarsius syrichta	ENSTSYG00000005241	4 retrocopies	retro_tsyr_1115, retro_tsyr_1208, retro_tsyr_1492, retro_tsyr_1780,
Tursiops truncatus	ENSTTRG00000003571	1 retrocopy	retro_ttru_202,