RetrogeneDB ID: retro_cpor_165

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_0:80235864..80236359(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000025020
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPIA
• Ensembl ID: ENSCPOG00000002632
• Aliases: None
• Description: Peptidyl-prolyl cis-trans isomerase [Source:UniProtKB/TrEMBL;Acc:H0UZ02]

Sequence

>retro_cpor_165
ATGGTCAACCCCACTGTGTTTGATGACATTGCTGCTGATGGTGAGCCCTTGGACCATGTCTCCTTCGAGCTGTATACAGA
CAAAGTTCCAAAGACAGCAGAAAACTTTTGTTCTCTGAGTACTGGAGAGGAAGGATTTGGTTATAAACGTTCCTACTTTC
ACAGAATTATTCCAGGATTTATGTGCCAGGGCAGTGACTTCACACACCACAATGGCATTGGTGGCAAGTCCATCCATGGG
GAGAAATTCGATGACAAGTACTTCATCCTGAAGCACACAGGTCCTGGCATCTTGTTCGTGGCAAATCCTGGGCCAAACAC
AATGGTCCCCAGTTTCTCATCTGCACTGCCAAGAGTGTGTGTATGGTTGGATGGCGAGCACGTGGTCTTTGGGAAGGTGA
AAGAGGGCATGACCACCATGGAGGCCATGGAGCACTTCGGGTCCAGGAATGGCAAGACCAGCAAGAAGATCACCAGCACC
AACTGTGGACAACTC

Alignment

ORF - retro_cpor_165 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.11 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVNPTVFFDIAADGEPLGRVSFELYADKVPKTAAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTR
          MVNPTVF.DIAADGEPL..VSFELY.DKVPKTA.ENF..LSTGE.GFGYK.S.FHRIIPGFMCQG.DFT.
Retrocopy MVNPTVFDDIAADGEPLDHVSFELYTDKVPKTA-ENFCSLSTGEEGFGYKRSYFHRIIPGFMCQGSDFTH

Parental  HNGTGGKSIYGEKFDDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVVFGKVKEGMNT
          HNG.GGKSI.GEKFDD..FILKHTGPGIL..AN.GPNT....F.........WLDG.HVVFGKVKEGM.T
Retrocopy HNGIGGKSIHGEKFDDKYFILKHTGPGILFVANPGPNTMVPSFSSALPRVCVWLDGEHVVFGKVKEGMTT

Parental  VEAMERFGSRNGKTSKKITITDCGQL
          .EAME.FGSRNGKTSKKIT.T.CGQL
Retrocopy MEAMEHFGSRNGKTSKKITSTNCGQL

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	464.33 RPM
SRP017611_kidney	0.00 RPM	448.59 RPM
SRP017611_liver	0.00 RPM	277.27 RPM
SRP040447_lung	0.00 RPM	585.22 RPM
SRP040447_skeletal_muscle	0.00 RPM	191.42 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_165 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_165 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 210 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012003	12 retrocopies	retro_btau_1005, retro_btau_1448, retro_btau_155, retro_btau_1696, retro_btau_1806, retro_btau_272, retro_btau_334, retro_btau_335, retro_btau_345, retro_btau_414, retro_btau_751, retro_btau_934,
Callithrix jacchus	ENSCJAG00000011969	54 retrocopies	retro_cjac_1065, retro_cjac_1080, retro_cjac_1083, retro_cjac_1092, retro_cjac_1097, retro_cjac_11, retro_cjac_1193, retro_cjac_1213, retro_cjac_1310, retro_cjac_1326, retro_cjac_1347, retro_cjac_1451, retro_cjac_147, retro_cjac_1678, retro_cjac_1710, retro_cjac_1760, retro_cjac_1782, retro_cjac_1982, retro_cjac_1989, retro_cjac_2043, retro_cjac_2060, retro_cjac_2062, retro_cjac_2118, retro_cjac_2286, retro_cjac_2327, retro_cjac_2376, retro_cjac_2425, retro_cjac_2426, retro_cjac_2479, retro_cjac_2540, retro_cjac_2688, retro_cjac_2863, retro_cjac_2881, retro_cjac_2977, retro_cjac_3073, retro_cjac_3077, retro_cjac_3101, retro_cjac_3196, retro_cjac_384, retro_cjac_4202, retro_cjac_4203, retro_cjac_501, retro_cjac_646, retro_cjac_649, retro_cjac_695, retro_cjac_704, retro_cjac_710, retro_cjac_714, retro_cjac_717, retro_cjac_755, retro_cjac_827, retro_cjac_834, retro_cjac_871, retro_cjac_971,
Cavia porcellus	ENSCPOG00000002632	11 retrocopies	retro_cpor_1152, retro_cpor_1284, retro_cpor_1395, retro_cpor_1493, retro_cpor_165 , retro_cpor_192, retro_cpor_251, retro_cpor_372, retro_cpor_642, retro_cpor_902, retro_cpor_960,
Cavia porcellus	ENSCPOG00000007365	1 retrocopy	retro_cpor_560,
Echinops telfairi	ENSETEG00000002186	21 retrocopies	retro_etel_115, retro_etel_1188, retro_etel_1292, retro_etel_1322, retro_etel_1670, retro_etel_1827, retro_etel_1875, retro_etel_1886, retro_etel_208, retro_etel_25, retro_etel_288, retro_etel_371, retro_etel_430, retro_etel_447, retro_etel_485, retro_etel_537, retro_etel_551, retro_etel_568, retro_etel_595, retro_etel_937, retro_etel_998,
Gorilla gorilla	ENSGGOG00000026298	4 retrocopies	retro_ggor_138, retro_ggor_15, retro_ggor_165, retro_ggor_28,
Loxodonta africana	ENSLAFG00000011345	1 retrocopy	retro_lafr_483,
Macaca mulatta	ENSMMUG00000016638	10 retrocopies	retro_mmul_1, retro_mmul_13, retro_mmul_132, retro_mmul_141, retro_mmul_161, retro_mmul_195, retro_mmul_245, retro_mmul_5, retro_mmul_56, retro_mmul_8,
Monodelphis domestica	ENSMODG00000016089	9 retrocopies	retro_mdom_1373, retro_mdom_1524, retro_mdom_1856, retro_mdom_1884, retro_mdom_215, retro_mdom_272, retro_mdom_29, retro_mdom_730, retro_mdom_85,
Mus musculus	ENSMUSG00000071866	2 retrocopies	retro_mmus_242, retro_mmus_285,
Oryctolagus cuniculus	ENSOCUG00000016662	3 retrocopies	retro_ocun_113, retro_ocun_1406, retro_ocun_237,
Otolemur garnettii	ENSOGAG00000027997	31 retrocopies	retro_ogar_1090, retro_ogar_1201, retro_ogar_1305, retro_ogar_1329, retro_ogar_1336, retro_ogar_1562, retro_ogar_1634, retro_ogar_1741, retro_ogar_1889, retro_ogar_1893, retro_ogar_1920, retro_ogar_1973, retro_ogar_1974, retro_ogar_1999, retro_ogar_21, retro_ogar_2246, retro_ogar_2265, retro_ogar_2397, retro_ogar_2401, retro_ogar_2440, retro_ogar_2484, retro_ogar_2794, retro_ogar_2907, retro_ogar_2924, retro_ogar_2938, retro_ogar_2948, retro_ogar_3072, retro_ogar_3187, retro_ogar_3210, retro_ogar_357, retro_ogar_743,
Pongo abelii	ENSPPYG00000017586	12 retrocopies	retro_pabe_1065, retro_pabe_1330, retro_pabe_186, retro_pabe_221, retro_pabe_2267, retro_pabe_2469, retro_pabe_2633, retro_pabe_2730, retro_pabe_2812, retro_pabe_3474, retro_pabe_631, retro_pabe_995,
Pongo abelii	ENSPPYG00000017587	4 retrocopies	retro_pabe_1118, retro_pabe_2202, retro_pabe_3311, retro_pabe_3602,
Rattus norvegicus	ENSRNOG00000006423	2 retrocopies	retro_rnor_360, retro_rnor_387,
Ictidomys tridecemlineatus	ENSSTOG00000010215	10 retrocopies	retro_itri_1073, retro_itri_1576, retro_itri_1683, retro_itri_1897, retro_itri_499, retro_itri_667, retro_itri_7, retro_itri_731, retro_itri_802, retro_itri_978,
Tarsius syrichta	ENSTSYG00000008973	23 retrocopies	retro_tsyr_1106, retro_tsyr_1266, retro_tsyr_1277, retro_tsyr_1530, retro_tsyr_1643, retro_tsyr_1816, retro_tsyr_1909, retro_tsyr_2040, retro_tsyr_2072, retro_tsyr_2097, retro_tsyr_388, retro_tsyr_400, retro_tsyr_408, retro_tsyr_430, retro_tsyr_459, retro_tsyr_478, retro_tsyr_481, retro_tsyr_507, retro_tsyr_641, retro_tsyr_705, retro_tsyr_760, retro_tsyr_847, retro_tsyr_924,