RetrogeneDB ID: retro_cpor_599

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_2:17114190..17114498(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDPK-A
• Ensembl ID: ENSCPOG00000008413
• Aliases: None
• Description: nucleoside diphosphate kinase A [Source:RefSeq peptide;Acc:NP_001166344]

Sequence

>retro_cpor_599
CTAGTGTGCGAGACCATCAAGCGGTTTGAGCAGAAGGGCTTTGCCTGGTGGCCATGAAGTTCATCCAGGCCTCGGAGGAG
CACCTGAAGCAGCACTTCAGCGACCTGAAGGTGCGGCCCTTCTGCCCGGTCTGGTGCAGTCAGTATGTGCACTCGGGGCC
GTGGCCAGGGTCTAGGAGGGGCTGAACGTGGTAAGGCGGGCCAAGCGGTGCTGGGTGAGGCCAACCCTGAGGACTCCAAG
CTAGGCGCCATCCGCGGAGACTTGTGCATTCAGTCGGCAGGAACATTGTCCACTGCAGTGACTCACTC

Alignment

ORF - retro_cpor_599 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.52 %
• Parental protein coverage: 64.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LVGEIIKRFEQKGFR-LVAMKFMRASEEHLKQHYSDLKERPF-FSGLVQYMHSGPVVAMVWEGLNVV-KT
          LV.E.IKRFEQKGF..LVAMKF..ASEEHLKQH.SDLK.RPF...GLVQ.......VA.V.EGLNVV.K.
Retrocopy LVCETIKRFEQKGFA<LVAMKFIQASEEHLKQHFSDLKVRPF<LPGLVQSVCALGAVARV*EGLNVV<KA

Parental  GRVMLGETNPADSKPGTIRGDFCIQ-VGRNIIHGSDSV
          G...LGE.NP.DSK.G.IRGD.CIQ.VGRNI.H.SDS.
Retrocopy GQAVLGEANPEDSKLGAIRGDLCIQ<VGRNIVHCSDSL

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	55.73 RPM
SRP017611_kidney	0.00 RPM	149.18 RPM
SRP017611_liver	0.00 RPM	82.40 RPM
SRP040447_lung	0.00 RPM	146.58 RPM
SRP040447_skeletal_muscle	0.00 RPM	144.69 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_599 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_599 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 5 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000023628	7 retrocopies	retro_cfam_117, retro_cfam_1645, retro_cfam_37, retro_cfam_676, retro_cfam_69, retro_cfam_832, retro_cfam_96,
Cavia porcellus	ENSCPOG00000006496	1 retrocopy	retro_cpor_1076,
Cavia porcellus	ENSCPOG00000008413	1 retrocopy	retro_cpor_599 ,
Echinops telfairi	ENSETEG00000005563	4 retrocopies	retro_etel_242, retro_etel_547, retro_etel_71, retro_etel_803,
Mus musculus	ENSMUSG00000091228	3 retrocopies	retro_mmus_2712, retro_mmus_3081, retro_mmus_581,