RetrogeneDB ID: retro_cpor_494

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_17:31457518..31457728(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPC2
• Ensembl ID: ENSCPOG00000003860
• Aliases: None
• Description: None

Sequence

>retro_cpor_494
TTGTCAGCCGCTGGTGTCCAGGGCCTGGGGGCCTTGCACCACTGGCTCCTCGATAGAGTGGAGATGATGCTGCTGAAGAA
ACTGAGGCCACTGTCCAACCACCCGGCAGGTCCCAGAACAGTATTTTTCTGGGCTCCAATGATGAAATGGAGCTTGACAT
GTGCTGGGTTGGCAGACATAGCCAGACCTGCAGAGAAGCTCAGCCCTGCA

Alignment

ORF - retro_cpor_494 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 55.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSAAGARGLRALHHRLLDRVELMLPEKLRPLYNHPAGPRTVFFWAPIMKWGLVCAGLADMARPAEKLSTA
          .SAAG..GL.ALHH.LLDRVE.ML..KLRPL.NHPAGPRTVFFWAP.MKW.L.CAGLAD.ARPAEKLS.A
Retrocopy LSAAGVQGLGALHHWLLDRVEMMLLKKLRPLSNHPAGPRTVFFWAPMMKWSLTCAGLADIARPAEKLSPA

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	18.23 RPM
SRP017611_kidney	0.00 RPM	48.68 RPM
SRP017611_liver	0.00 RPM	50.93 RPM
SRP040447_lung	0.00 RPM	17.96 RPM
SRP040447_skeletal_muscle	0.00 RPM	89.19 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_494 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_494 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 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006273	2 retrocopies	retro_amel_527, retro_amel_987,
Bos taurus	ENSBTAG00000020968	2 retrocopies	retro_btau_1459, retro_btau_557,
Canis familiaris	ENSCAFG00000015358	2 retrocopies	retro_cfam_1350, retro_cfam_1897,
Choloepus hoffmanni	ENSCHOG00000007752	6 retrocopies	retro_chof_1286, retro_chof_1294, retro_chof_2021, retro_chof_23, retro_chof_47, retro_chof_835,
Callithrix jacchus	ENSCJAG00000016985	1 retrocopy	retro_cjac_4207,
Cavia porcellus	ENSCPOG00000003860	1 retrocopy	retro_cpor_494 ,
Dasypus novemcinctus	ENSDNOG00000011180	1 retrocopy	retro_dnov_475,
Microcebus murinus	ENSMICG00000011691	5 retrocopies	retro_mmur_1158, retro_mmur_1503, retro_mmur_317, retro_mmur_348, retro_mmur_986,
Myotis lucifugus	ENSMLUG00000011873	1 retrocopy	retro_mluc_610,
Macaca mulatta	ENSMMUG00000010387	1 retrocopy	retro_mmul_432,
Mus musculus	ENSMUSG00000026568	3 retrocopies	retro_mmus_1651, retro_mmus_578, retro_mmus_647,
Otolemur garnettii	ENSOGAG00000003130	3 retrocopies	retro_ogar_1494, retro_ogar_1992, retro_ogar_2653,
Sus scrofa	ENSSSCG00000006304	1 retrocopy	retro_sscr_241,
Tupaia belangeri	ENSTBEG00000014189	9 retrocopies	retro_tbel_1099, retro_tbel_1446, retro_tbel_1614, retro_tbel_1847, retro_tbel_2174, retro_tbel_3168, retro_tbel_433, retro_tbel_4444, retro_tbel_734,
Tarsius syrichta	ENSTSYG00000010251	3 retrocopies	retro_tsyr_10, retro_tsyr_141, retro_tsyr_1810,
Tursiops truncatus	ENSTTRG00000008566	1 retrocopy	retro_ttru_1743,
Vicugna pacos	ENSVPAG00000010556	1 retrocopy	retro_vpac_51,