RetrogeneDB ID: retro_cpor_1000

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_39:17683508..17683910(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL13A
• Ensembl ID: ENSCPOG00000012417
• Aliases: None
• Description: None

Sequence

>retro_cpor_1000
TCTTGTGGCCCCTAACACTTCCAAGCCCCGAACTGCATCTTCTGGCAGGCTGTGTCAGGGATGCTGCCCCATAAGACCAA
GCGAGGCTAAACTGCCCTGGACTGCCTCAAGGTGTTTGATGGCATCCCACCACCCTATGACAAGAAAAAGCAAATGGTAG
TTCCTGGCACCCTCAAAGTTGTGCACCTAAAGCCAATGAGGAAGTTTTCCTACTTGGGCCACCTGGCCCATGAGGTTGGC
TGGAAGTACCAAGTGGTGACAACCACTCTGGAGAAGAGGAAGGAGAAGGCCAAGATCCACTACCAGAAGAAGCACATCAT
GAGGCTACGGAAACAGGCTGAAAAGAATGTGGAGGAGAAAATTGGCAGGTTCACAGAGGTCCTCAAGACACACAGACTTC
TG

Alignment

ORF - retro_cpor_1000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.15 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRGPYHFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPAALKVVRLKPTRKFA
          S.GP.HF.AP..IFW..V.GMLPHKTKRG..ALD.LKVFDGIPPPYDKKK.MVVP..LKVV.LKP.RKF.
Retrocopy SCGP*HFQAPNCIFWQAVSGMLPHKTKRG*TALDCLKVFDGIPPPYDKKKQMVVPGTLKVVHLKPMRKFS

Parental  YLGRLAHEVGWKYQAVTATLEEKRKEKAKIHYRKKKQIMRLRKQAEKNVEKKIGKFTEVLKTHGLL
          YLG.LAHEVGWKYQ.VT.TL.EKRKEKAKIHY..KK.IMRLRKQAEKNVE.KIG.FTEVLKTH.LL
Retrocopy YLGHLAHEVGWKYQVVTTTL-EKRKEKAKIHY-QKKHIMRLRKQAEKNVEEKIGRFTEVLKTHRLL

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	128.66 RPM
SRP017611_kidney	0.00 RPM	217.85 RPM
SRP017611_liver	0.00 RPM	158.83 RPM
SRP040447_lung	0.03 RPM	502.00 RPM
SRP040447_skeletal_muscle	0.00 RPM	485.46 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1000 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1000 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 20 parental genes, and 120 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005296	3 retrocopies	retro_btau_1251, retro_btau_719, retro_btau_789,
Canis familiaris	ENSCAFG00000029892	3 retrocopies	retro_cfam_1772, retro_cfam_924, retro_cfam_976,
Callithrix jacchus	ENSCJAG00000000072	16 retrocopies	retro_cjac_1130, retro_cjac_1706, retro_cjac_182, retro_cjac_197, retro_cjac_1997, retro_cjac_2170, retro_cjac_2322, retro_cjac_2467, retro_cjac_2468, retro_cjac_2665, retro_cjac_2699, retro_cjac_2755, retro_cjac_3009, retro_cjac_664, retro_cjac_941, retro_cjac_972,
Cavia porcellus	ENSCPOG00000012417	2 retrocopies	retro_cpor_1000 , retro_cpor_888,
Erinaceus europaeus	ENSEEUG00000014071	6 retrocopies	retro_eeur_168, retro_eeur_310, retro_eeur_315, retro_eeur_484, retro_eeur_562, retro_eeur_618,
Echinops telfairi	ENSETEG00000017076	2 retrocopies	retro_etel_46, retro_etel_853,
Felis catus	ENSFCAG00000009194	4 retrocopies	retro_fcat_1197, retro_fcat_1649, retro_fcat_324, retro_fcat_548,
Gorilla gorilla	ENSGGOG00000002932	11 retrocopies	retro_ggor_12, retro_ggor_1739, retro_ggor_214, retro_ggor_2271, retro_ggor_2737, retro_ggor_334, retro_ggor_6, retro_ggor_615, retro_ggor_627, retro_ggor_846, retro_ggor_869,
Myotis lucifugus	ENSMLUG00000004945	10 retrocopies	retro_mluc_1015, retro_mluc_1342, retro_mluc_1836, retro_mluc_1894, retro_mluc_2219, retro_mluc_2221, retro_mluc_2427, retro_mluc_2471, retro_mluc_2506, retro_mluc_675,
Macaca mulatta	ENSMMUG00000007551	14 retrocopies	retro_mmul_1100, retro_mmul_1256, retro_mmul_1638, retro_mmul_1756, retro_mmul_2179, retro_mmul_2249, retro_mmul_2352, retro_mmul_2399, retro_mmul_296, retro_mmul_500, retro_mmul_520, retro_mmul_547, retro_mmul_837, retro_mmul_924,
Mus musculus	ENSMUSG00000074129	3 retrocopies	retro_mmus_1129, retro_mmus_1334, retro_mmus_20,
Oryctolagus cuniculus	ENSOCUG00000025258	9 retrocopies	retro_ocun_1038, retro_ocun_1077, retro_ocun_1392, retro_ocun_1462, retro_ocun_304, retro_ocun_674, retro_ocun_756, retro_ocun_786, retro_ocun_972,
Otolemur garnettii	ENSOGAG00000004625	7 retrocopies	retro_ogar_1496, retro_ogar_211, retro_ogar_2254, retro_ogar_3148, retro_ogar_54, retro_ogar_596, retro_ogar_612,
Ochotona princeps	ENSOPRG00000001194	3 retrocopies	retro_opri_316, retro_opri_764, retro_opri_806,
Pongo abelii	ENSPPYG00000010251	1 retrocopy	retro_pabe_148,
Pan troglodytes	ENSPTRG00000011298	1 retrocopy	retro_ptro_31,
Rattus norvegicus	ENSRNOG00000020618	10 retrocopies	retro_rnor_1073, retro_rnor_1112, retro_rnor_1212, retro_rnor_1292, retro_rnor_1357, retro_rnor_1742, retro_rnor_564, retro_rnor_593, retro_rnor_665, retro_rnor_988,
Sus scrofa	ENSSSCG00000003166	4 retrocopies	retro_sscr_290, retro_sscr_300, retro_sscr_392, retro_sscr_743,
Tarsius syrichta	ENSTSYG00000008791	4 retrocopies	retro_tsyr_1363, retro_tsyr_437, retro_tsyr_620, retro_tsyr_920,
Tursiops truncatus	ENSTTRG00000005485	7 retrocopies	retro_ttru_1304, retro_ttru_1736, retro_ttru_629, retro_ttru_735, retro_ttru_833, retro_ttru_971, retro_ttru_995,