RetrogeneDB ID: retro_cpor_879

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_30:25689254..25689595(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000013520
• Aliases: None
• Description: None

Sequence

>retro_cpor_879
TTGCCTATGTTCATCTTGAATATCAATGTGCCCCGCAGTCCATGTCGGAGAGATTCCTCTCCGAACTCACGCAGCAGCTT
GCGCAGGCCACCGGCAAGCCCACCCAGTACATCACAGTGCATGTGCTCCCAGACCAGCTCATGACCTTCACGGGCTCATG
GAAGCCATGCATGCTCTGCAGCCTGCACAGCATCCGCAAGATAGGTTAAGTGCTGAATTGCTCCTACAGCAAGCTGTTGT
GTGGTCTGTTGTCCTAGTGCCTGTGCATCAGTCCCGATAGGGTTTATATCAACTATTATGACATCAATGCTGCCAACATG
AGCTTGAAAAGCTCCACCTTC

Alignment

ORF - retro_cpor_879 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.65 %
• Parental protein coverage: 99.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPMFILNTNVPRS-SVPDGFLSELTQQLAQATGKPAQYIAVHVVPDQLMTFAGSSEPCALCSLHSIGKIG
          .PMFILN.NVPRS.S....FLSELTQQLAQATGKP.QYI.VHV.PDQLMTF.GS..PC.LCSLHSI.KIG
Retrocopy LPMFILNINVPRS<SMSERFLSELTQQLAQATGKPTQYITVHVLPDQLMTFTGSWKPCMLCSLHSIRKIG

Parental  GAQNRSYSKLLCGLLSERLRISPDRVYINYYDMNAANVGWNSTTF
          ...N.SYSKLLCGLLS..L.ISPDRVYINYYD.NAAN....S.TF
Retrocopy *VLNCSYSKLLCGLLS*CLCISPDRVYINYYDINAANMSLKSSTF

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	46.19 RPM
SRP017611_kidney	0.00 RPM	85.11 RPM
SRP017611_liver	0.00 RPM	26.51 RPM
SRP040447_lung	0.00 RPM	45.20 RPM
SRP040447_skeletal_muscle	0.00 RPM	34.00 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_879 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_879 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 8 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010668	3 retrocopies	retro_cjac_2903, retro_cjac_3132, retro_cjac_357,
Cavia porcellus	ENSCPOG00000013520	1 retrocopy	retro_cpor_879 ,
Dasypus novemcinctus	ENSDNOG00000014555	1 retrocopy	retro_dnov_36,
Equus caballus	ENSECAG00000012792	1 retrocopy	retro_ecab_1122,
Echinops telfairi	ENSETEG00000012052	3 retrocopies	retro_etel_2001, retro_etel_2046, retro_etel_509,
Mus musculus	ENSMUSG00000033307	8 retrocopies	retro_mmus_1573, retro_mmus_1759, retro_mmus_1878, retro_mmus_2182, retro_mmus_2444, retro_mmus_3016, retro_mmus_3315, retro_mmus_489,
Ochotona princeps	ENSOPRG00000012184	1 retrocopy	retro_opri_968,
Rattus norvegicus	ENSRNOG00000006589	6 retrocopies	retro_rnor_137, retro_rnor_1608, retro_rnor_1644, retro_rnor_2263, retro_rnor_31, retro_rnor_361,