RetrogeneDB ID: retro_cpor_64

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_23:13048709..13049354(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000015183
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPL10
• Ensembl ID: ENSCPOG00000002355
• Aliases: None
• Description: None

Sequence

>retro_cpor_64
ATGGGTCGCCGGCCGGCTCGCTGTTACCGTTACTGTAAAAACAAGCCATACCCCAAGTCTCGTTTCTGCCGGGGTGTCCC
GAATGCGAAGATTCACATCTTTGACCTGGGGCGGAAGAAGGCCAAAGTGGACGAGTTCCCACTGTGTGCCCACATGGTAT
CCGGTGAACACGAGCAGTTGTCGTCAGAAGCCCTGGAGGCCGCCCGCATCTGTGCCAACAAGTACATGGTGAAGACCTGC
GGCAAAGATGGCTTTCACATCCGGGTGCGGCTCCACCCCTTCCACGTCATCCGCATCAACAAGATGTTGTCCTGTGCTGG
AGCTGACAGGCTGCAGACGGGGATGCGCGGTGCCTTTGGGAAGCCCCAGGGCACGGTGGCCAGGGTCCACATTGGCCAGG
TCATCATGTCCATCCGCACCAAGCTGCTGAACAAGAAGCATGTGATCGAAGCCTTGCGCAGGGCCAAGTTCAAGTTCCCT
GGACGCCAGAAAATCCATATCTCCAAGAAGTGGGGCTTTACCAAGTACAACGCTGATGAATTTGAAGAACAGATGGCTGC
GAAGCGCCTGCTCCCTGATGGTTGTGGAGTCAAGTACATCCCCCGGCGTGGCCCTTTAGACAAGTGGAGGGCACTGTGCT
CTTGA

Alignment

ORF - retro_cpor_64 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.09 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEAALEAAR
          MGRRPARCYRYCKNKPYPKSRFCRGVP.AKI.IFDLGRKKAKVDEFPLC.HMVS.E.EQLSSEA.LEAAR
Retrocopy MGRRPARCYRYCKNKPYPKSRFCRGVPNAKIHIFDLGRKKAKVDEFPLCAHMVSGEHEQLSSEA-LEAAR

Parental  ICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIR
          ICANKYMVK.CGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIR
Retrocopy ICANKYMVKTCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIR

Parental  TKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLDKW
          TKL.NK.HVIEALRRAKFKFPGRQKIHISKKWGFTK.NADEFE...A.KRL.PDGCGVKYIP.RGPLDKW
Retrocopy TKLLNKKHVIEALRRAKFKFPGRQKIHISKKWGFTKYNADEFEEQMAAKRLLPDGCGVKYIPRRGPLDKW

Parental  RALHS
          RAL.S
Retrocopy RALCS

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	158.98 RPM
SRP017611_kidney	0.00 RPM	274.70 RPM
SRP017611_liver	0.00 RPM	255.50 RPM
SRP040447_lung	0.00 RPM	518.89 RPM
SRP040447_skeletal_muscle	0.00 RPM	535.80 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_64 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_64 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 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007454	2 retrocopies	retro_btau_140, retro_btau_99,
Cavia porcellus	ENSCPOG00000002355	1 retrocopy	retro_cpor_64 ,
Equus caballus	ENSECAG00000017154	1 retrocopy	retro_ecab_113,
Macropus eugenii	ENSMEUG00000013163	3 retrocopies	retro_meug_1839, retro_meug_5, retro_meug_547,
Microcebus murinus	ENSMICG00000004658	2 retrocopies	retro_mmur_1077, retro_mmur_4,
Monodelphis domestica	ENSMODG00000008731	2 retrocopies	retro_mdom_177, retro_mdom_829,
Mustela putorius furo	ENSMPUG00000009320	3 retrocopies	retro_mputfur_1405, retro_mputfur_54, retro_mputfur_84,
Mus musculus	ENSMUSG00000008682	1 retrocopy	retro_mmus_71,
Otolemur garnettii	ENSOGAG00000000099	3 retrocopies	retro_ogar_293, retro_ogar_2995, retro_ogar_3284,
Ictidomys tridecemlineatus	ENSSTOG00000011857	2 retrocopies	retro_itri_174, retro_itri_506,