RetrogeneDB ID: retro_cpor_1082

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_45:1442165..1442462(+)
• Located in intron of: ENSCPOG00000013806

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL51
• Ensembl ID: ENSCPOG00000008478
• Aliases: None
• Description: None

Sequence

>retro_cpor_1082
AGGAGCCTGTGCAGCTGGGTGACCTTGGCTTGCAGAAACTTCTCAGTGGGAGTTCCTGGATTATCCTGTATAAGGCTCAC
CCAGCTGCCTCCCAAAGTGGTTGATTCTTGGAATAAGAGGGTCGTGTTTGGAGTATATGACAACATCAGGATTCTGAGAG
ACCTTGAAAAGCACCTCGAAGACCTGATTACAGGCCCCATATGACTTCAAGGTTGGAAGGGAAATGAATTGCAGCAATGG
ATCCAAAAGAAGAAAATGGTTGGAAATAGAATGTTCACTGATGACCTGCACAACCTT

Alignment

ORF - retro_cpor_1082 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.0 %
• Parental protein coverage: 78.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGLCGLVTLACRNFSLGVPGLSRIRLTLPPPKVVDRWNEKRAMFGVYDNIGILGDFEKHPKDLIRGPRWL
          R.LC..VTLACRNFS.GVPGLS.IRLT..PPKVVD.WN.KR..FGVYDNI.IL.D.EKH..DLI.GP..L
Retrocopy RSLCSWVTLACRNFSVGVPGLSCIRLTQLPPKVVDSWN-KRVVFGVYDNIRILRDLEKHLEDLITGPI*L

Parental  RGWKGNELQRCIRKKKMVGNRMFIDDLHNL
          .GWKGNELQ..I.KKKMVGNRMF.DDLHNL
Retrocopy QGWKGNELQQWIQKKKMVGNRMFTDDLHNL

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	0.06 RPM	21.05 RPM
SRP017611_kidney	0.00 RPM	21.57 RPM
SRP017611_liver	0.00 RPM	21.63 RPM
SRP040447_lung	0.00 RPM	9.63 RPM
SRP040447_skeletal_muscle	0.00 RPM	31.43 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1082 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1082 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014729	1 retrocopy	retro_btau_1609,
Callithrix jacchus	ENSCJAG00000018232	1 retrocopy	retro_cjac_548,
Cavia porcellus	ENSCPOG00000008478	1 retrocopy	retro_cpor_1082 ,
Loxodonta africana	ENSLAFG00000002106	2 retrocopies	retro_lafr_1157, retro_lafr_845,
Mus musculus	ENSMUSG00000030335	2 retrocopies	retro_mmus_1967, retro_mmus_2607,
Pteropus vampyrus	ENSPVAG00000012566	1 retrocopy	retro_pvam_534,
Rattus norvegicus	ENSRNOG00000019165	2 retrocopies	retro_rnor_2582, retro_rnor_926,
Tupaia belangeri	ENSTBEG00000000936	2 retrocopies	retro_tbel_3219, retro_tbel_3408,