RetrogeneDB ID: retro_cpor_1454

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_87:1239909..1240210(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBA52
• Ensembl ID: ENSCPOG00000000351
• Aliases: None
• Description: None

Sequence

>retro_cpor_1454
ACTCTCAAGGTTGAGACCAGTAACACTATAGAAAATGTCAAAGCCCAAATCCAAGTCAAGTAGCGCACGTGACCTACTAG
CAACGTCTGTATTGTATTTGCCAGTGAACAGCTAAAGGATGGCCACACTGTCTCTGAATCCAACATCTAGAAAGAGCCCA
GCCTGCATTTGGTGTTCTTCCTCCGAGGCAGTATTACTGAGCCTTTCTTGTGCCAGCCTGCCCAAGAAGTACAACTGTGA
CAAAATGATCTGCCTCTGGTGTAATGCCTGCCAGCAGCCCTGTGCGGTCAACTGCAGCAGG

Alignment

ORF - retro_cpor_1454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.43 %
• Parental protein coverage: 77.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TLEVEPSDTIENVKAKIQDK-EGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGIIEPSL
          TL.VE.S.TIENVKA.IQ.K....P.......FA..QL.DG.T.S..NI.KE..LHLV..LRG.I.EP.L
Retrocopy TLKVETSNTIENVKAQIQVK*RT*PTSNVCIVFASEQLKDGHTVSESNI*KEPSLHLVFFLRGSITEPFL

Parental  RQLAQ-KYNCDKMICRKCYARLHPRAVNCRK
          .Q.AQ.KYNCDKMIC..C.A...P.AVNC..
Retrocopy CQPAQ>KYNCDKMICLWCNACQQPCAVNCSR

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	77.01 RPM
SRP017611_kidney	0.00 RPM	140.49 RPM
SRP017611_liver	0.00 RPM	86.66 RPM
SRP040447_lung	0.05 RPM	174.70 RPM
SRP040447_skeletal_muscle	0.00 RPM	175.45 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1454 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1454 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 109 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000351	3 retrocopies	retro_cpor_1454 , retro_cpor_1471, retro_cpor_1502,
Echinops telfairi	ENSETEG00000003392	35 retrocopies	retro_etel_1121, retro_etel_113, retro_etel_1165, retro_etel_1229, retro_etel_1520, retro_etel_1521, retro_etel_1598, retro_etel_1618, retro_etel_1623, retro_etel_1644, retro_etel_1657, retro_etel_1707, retro_etel_1709, retro_etel_174, retro_etel_1756, retro_etel_1760, retro_etel_1785, retro_etel_1854, retro_etel_196, retro_etel_2027, retro_etel_2101, retro_etel_2123, retro_etel_2158, retro_etel_2166, retro_etel_268, retro_etel_376, retro_etel_386, retro_etel_406, retro_etel_660, retro_etel_690, retro_etel_70, retro_etel_755, retro_etel_807, retro_etel_843, retro_etel_859,
Gorilla gorilla	ENSGGOG00000004630	8 retrocopies	retro_ggor_1021, retro_ggor_1045, retro_ggor_1265, retro_ggor_1835, retro_ggor_2579, retro_ggor_2687, retro_ggor_2782, retro_ggor_905,
Latimeria chalumnae	ENSLACG00000008132	1 retrocopy	retro_lcha_11,
Macropus eugenii	ENSMEUG00000013159	5 retrocopies	retro_meug_1812, retro_meug_1868, retro_meug_441, retro_meug_513, retro_meug_750,
Myotis lucifugus	ENSMLUG00000029594	5 retrocopies	retro_mluc_1995, retro_mluc_2057, retro_mluc_2203, retro_mluc_44, retro_mluc_829,
Macaca mulatta	ENSMMUG00000016085	7 retrocopies	retro_mmul_1184, retro_mmul_1580, retro_mmul_1625, retro_mmul_2183, retro_mmul_2311, retro_mmul_232, retro_mmul_896,
Mustela putorius furo	ENSMPUG00000015527	8 retrocopies	retro_mputfur_1059, retro_mputfur_1119, retro_mputfur_1126, retro_mputfur_382, retro_mputfur_516, retro_mputfur_713, retro_mputfur_78, retro_mputfur_945,
Mus musculus	ENSMUSG00000090137	3 retrocopies	retro_mmus_101, retro_mmus_129, retro_mmus_31,
Pongo abelii	ENSPPYG00000009746	2 retrocopies	retro_pabe_111, retro_pabe_3291,
Pteropus vampyrus	ENSPVAG00000024217	19 retrocopies	retro_pvam_1029, retro_pvam_1102, retro_pvam_1146, retro_pvam_1164, retro_pvam_1320, retro_pvam_1325, retro_pvam_1361, retro_pvam_1434, retro_pvam_1447, retro_pvam_211, retro_pvam_327, retro_pvam_517, retro_pvam_528, retro_pvam_600, retro_pvam_632, retro_pvam_655, retro_pvam_749, retro_pvam_987, retro_pvam_994,
Sorex araneus	ENSSARG00000000984	11 retrocopies	retro_sara_145, retro_sara_164, retro_sara_192, retro_sara_256, retro_sara_281, retro_sara_331, retro_sara_344, retro_sara_599, retro_sara_67, retro_sara_687, retro_sara_94,
Ictidomys tridecemlineatus	ENSSTOG00000004678	1 retrocopy	retro_itri_49,
Xiphophorus maculatus	ENSXMAG00000003911	1 retrocopy	retro_xmac_6,