RetrogeneDB ID: retro_cpor_1415

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_8:27502114..27502885(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL8
• Ensembl ID: ENSCPOG00000003854
• Aliases: None
• Description: None

Sequence

>retro_cpor_1415
ATGGGCCACGTGATCCGTGGACAGAGGAAGGGTGCTGGCTCTGTGTTTCATGTGCACGTGAAACATTGCAAGGGAGCTGT
TCGGCTACGTGCCGTGGACTTCGCAGAGCTGCACGGCTACATCAAGGGGATCGTGAAGGACATCATCCACGACCCAGGCC
GCAGTGCACCGCTCACTAAGGTGGTCTTCCGAGATCCGTACCAATTCAAGAAGCATACGGAGCTGTTCATTGCCGCCGAG
GGCATCCACATGGGCCAATTTGTGTACTGCGGCAAGAAGGCCCAACTCAACGCTGGCAATGTTCTCCCTGTGGGCACCAT
GCCTGAGAGGACCACTGTGTGCTGCTTGGAGGAGAAGGCTGGAGACAGGGGCAAGCTGACCTGAACCTCTGGCAATTATG
CCACAGTCATTTCTCACAACCCTGAAACCAAAAAGACCAGAGTGAAGCTGCCCTCAGGTTCCAAGAAGGTCATCTCCTCT
GCCAACAGAGCTGTTGTTGGTGTAGTAGCTGATGGGGGTAGAATTGATAAACCTATTTTGAAGGCTGGTCGAGCCTACCA
CAAATACAAGGCAAAGAGGAACTGCTGGCCACGTGTATGTGGTGTGGCCATGAATCCCGTGGAGCATCCTTTTGGAGGTG
GTAACCACCAGCACATTGGCAAACCCTCAACTATCCATAGAGATGCCCCTGCAGGACGCAAAGTGGGTCTTATTGCTGCT
CGCAGGGCTGGGCGACTCCGTGGAATCAAGACTGTGCAAGAGAAAGAGAAT

Alignment

ORF - retro_cpor_1415 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.05 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKVVFRDPYRFK
          MG.VIRGQRKGAGSVF..HVKH.KGA.RLRAVDFAE.HGYIKGIVKDIIHDPGR.APL.KVVFRDPY.FK
Retrocopy MGHVIRGQRKGAGSVFHVHVKHCKGAVRLRAVDFAELHGYIKGIVKDIIHDPGRSAPLTKVVFRDPYQFK

Parental  KRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPGDRGKLARASGNYATVISHN
          K.TELFIAAEGIH.GQFVYCGKKAQLN.GNVLPVGTMPE.T.VCCLEEK.GDRGKL...SGNYATVISHN
Retrocopy KHTELFIAAEGIHMGQFVYCGKKAQLNAGNVLPVGTMPERTTVCCLEEKAGDRGKLT*TSGNYATVISHN

Parental  PETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILKAGRAYHKYKAKRNCWPRVRGVAMNPVEHP
          PETKKTRVKLPSGSKKVISSANRAVVGVVA.GGRIDKPILKAGRAYHKYKAKRNCWPRV.GVAMNPVEHP
Retrocopy PETKKTRVKLPSGSKKVISSANRAVVGVVADGGRIDKPILKAGRAYHKYKAKRNCWPRVCGVAMNPVEHP

Parental  FGGGNHQHIGKPSTIRRDAPAGRKVGLIAARRTGRLRGTKTVQEKEN
          FGGGNHQHIGKPSTI.RDAPAGRKVGLIAARR.GRLRG.KTVQEKEN
Retrocopy FGGGNHQHIGKPSTIHRDAPAGRKVGLIAARRAGRLRGIKTVQEKEN

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	0.35 RPM	160.13 RPM
SRP017611_kidney	0.21 RPM	262.87 RPM
SRP017611_liver	0.04 RPM	159.18 RPM
SRP040447_lung	0.40 RPM	425.96 RPM
SRP040447_skeletal_muscle	0.20 RPM	388.25 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1415 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1415 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017933	1 retrocopy	retro_acar_31,
Bos taurus	ENSBTAG00000026327	1 retrocopy	retro_btau_96,
Canis familiaris	ENSCAFG00000001677	1 retrocopy	retro_cfam_1132,
Callithrix jacchus	ENSCJAG00000021388	4 retrocopies	retro_cjac_1109, retro_cjac_1169, retro_cjac_1579, retro_cjac_2047,
Cavia porcellus	ENSCPOG00000003854	2 retrocopies	retro_cpor_1006, retro_cpor_1415 ,
Dasypus novemcinctus	ENSDNOG00000009300	2 retrocopies	retro_dnov_2505, retro_dnov_503,
Macaca mulatta	ENSMMUG00000013379	2 retrocopies	retro_mmul_1470, retro_mmul_1531,
Mustela putorius furo	ENSMPUG00000006022	1 retrocopy	retro_mputfur_1517,
Nomascus leucogenys	ENSNLEG00000010952	2 retrocopies	retro_nleu_1603, retro_nleu_594,
Oryctolagus cuniculus	ENSOCUG00000024716	1 retrocopy	retro_ocun_146,
Rattus norvegicus	ENSRNOG00000048523	2 retrocopies	retro_rnor_122, retro_rnor_239,