RetrogeneDB ID: retro_cpor_404

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_141:813970..814310(-)
• Located in intron of: ENSCPOG00000007358

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS20
• Ensembl ID: ENSCPOG00000011697
• Aliases: None
• Description: None

Sequence

>retro_cpor_404
TTTACAGATACCGGAAAGACACCCATGGGACCCAAGGTGGCGATTCACTGAATTAAGATTAGATTCAGCAGCCACTGCAA
GAAATTCCTGGAAAAGGGGTGTAGTGACTTCACCAGAGGTATAAAGGAAAAGAACTGCAAAGTAAAAGGACTCAATCGCA
CACCAAGTCCTTGAGAATCACTATAAGAAAAACGTCTTGTGGTGAAGGCTCTAAGACCTGGGATTGTTTCACATGAGACA
CTACAAGCAACTTCTTGATTTTCACCCTGCTTCTGAGATTGTTTAGCAGATTACTTCCAACAGTGCTGAGCCAGGAGAGG
AGGCTGAAGTCACCATAGCA

Alignment

ORF - retro_cpor_404 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.68 %
• Parental protein coverage: 96.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FKDTGKTPVEPEVAIHRIRITLTSRNVKSLEKVCADLIRGAKE-KNLKVKGPVRMPTKTLRITTRKTPCG
          F.DTGKTP..P.VAIH.I.I...S...K.LEK.C.D..RG.KE.K.L..K......TK.LRIT.RKT.CG
Retrocopy FTDTGKTPMGPKVAIH*IKIRFSSHCKKFLEKGCSDFTRGIKE<KELQSKR-TQSHTKSLRITIRKTSCG

Parental  EGSKTWD-RFQMRIHKRLIDLHSPSEIVKQITSISIEPGVEVEVTIA
          EGSKTWD..F.MR..K.L.D.H..SEIV.QITS.S.EPG.E.EVTIA
Retrocopy EGSKTWD<LFHMRHYKQLLDFHPASEIV*QITSNSAEPGEEAEVTIA

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	84.43 RPM
SRP017611_kidney	0.00 RPM	154.94 RPM
SRP017611_liver	0.00 RPM	92.19 RPM
SRP040447_lung	0.00 RPM	174.78 RPM
SRP040447_skeletal_muscle	0.00 RPM	186.40 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_404 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_404 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 14 parental genes, and 149 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006087	17 retrocopies	retro_amel_1067, retro_amel_1142, retro_amel_1146, retro_amel_1245, retro_amel_1405, retro_amel_1409, retro_amel_1442, retro_amel_1579, retro_amel_1619, retro_amel_1825, retro_amel_281, retro_amel_299, retro_amel_437, retro_amel_495, retro_amel_599, retro_amel_709, retro_amel_98,
Canis familiaris	ENSCAFG00000029884	20 retrocopies	retro_cfam_1144, retro_cfam_1247, retro_cfam_1287, retro_cfam_1367, retro_cfam_1409, retro_cfam_1472, retro_cfam_1633, retro_cfam_1646, retro_cfam_1688, retro_cfam_1719, retro_cfam_1810, retro_cfam_1964, retro_cfam_1978, retro_cfam_1992, retro_cfam_2008, retro_cfam_2193, retro_cfam_559, retro_cfam_666, retro_cfam_672, retro_cfam_949,
Callithrix jacchus	ENSCJAG00000016631	4 retrocopies	retro_cjac_3017, retro_cjac_319, retro_cjac_667, retro_cjac_749,
Cavia porcellus	ENSCPOG00000011697	10 retrocopies	retro_cpor_1002, retro_cpor_1016, retro_cpor_1064, retro_cpor_1104, retro_cpor_1507, retro_cpor_404 , retro_cpor_499, retro_cpor_533, retro_cpor_544, retro_cpor_717,
Echinops telfairi	ENSETEG00000003394	3 retrocopies	retro_etel_16, retro_etel_1814, retro_etel_2067,
Gorilla gorilla	ENSGGOG00000001837	21 retrocopies	retro_ggor_1074, retro_ggor_1149, retro_ggor_1581, retro_ggor_1640, retro_ggor_1751, retro_ggor_1768, retro_ggor_1908, retro_ggor_2193, retro_ggor_2227, retro_ggor_2639, retro_ggor_2712, retro_ggor_2751, retro_ggor_2809, retro_ggor_2857, retro_ggor_410, retro_ggor_707, retro_ggor_727, retro_ggor_838, retro_ggor_851, retro_ggor_909, retro_ggor_977,
Loxodonta africana	ENSLAFG00000002515	8 retrocopies	retro_lafr_353, retro_lafr_378, retro_lafr_537, retro_lafr_719, retro_lafr_730, retro_lafr_851, retro_lafr_865, retro_lafr_880,
Myotis lucifugus	ENSMLUG00000029059	2 retrocopies	retro_mluc_1187, retro_mluc_546,
Macaca mulatta	ENSMMUG00000021314	1 retrocopy	retro_mmul_16,
Mustela putorius furo	ENSMPUG00000010452	15 retrocopies	retro_mputfur_1094, retro_mputfur_1188, retro_mputfur_1313, retro_mputfur_1366, retro_mputfur_1374, retro_mputfur_1432, retro_mputfur_238, retro_mputfur_249, retro_mputfur_320, retro_mputfur_418, retro_mputfur_424, retro_mputfur_433, retro_mputfur_620, retro_mputfur_77, retro_mputfur_819,
Nomascus leucogenys	ENSNLEG00000001214	19 retrocopies	retro_nleu_1013, retro_nleu_1343, retro_nleu_1447, retro_nleu_1566, retro_nleu_1794, retro_nleu_1798, retro_nleu_1805, retro_nleu_1818, retro_nleu_2059, retro_nleu_2159, retro_nleu_2654, retro_nleu_2659, retro_nleu_2750, retro_nleu_2786, retro_nleu_2819, retro_nleu_2843, retro_nleu_3066, retro_nleu_382, retro_nleu_41,
Otolemur garnettii	ENSOGAG00000007760	10 retrocopies	retro_ogar_1337, retro_ogar_1759, retro_ogar_177, retro_ogar_1927, retro_ogar_2203, retro_ogar_2286, retro_ogar_2576, retro_ogar_309, retro_ogar_310, retro_ogar_900,
Rattus norvegicus	ENSRNOG00000008555	7 retrocopies	retro_rnor_142, retro_rnor_155, retro_rnor_192, retro_rnor_288, retro_rnor_381, retro_rnor_401, retro_rnor_58,
Sus scrofa	ENSSSCG00000006249	12 retrocopies	retro_sscr_1123, retro_sscr_30, retro_sscr_567, retro_sscr_575, retro_sscr_577, retro_sscr_585, retro_sscr_611, retro_sscr_646, retro_sscr_691, retro_sscr_708, retro_sscr_724, retro_sscr_838,