RetrogeneDB ID: retro_cpor_1060

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_42:3781980..3782347(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF5A2
• Ensembl ID: ENSCPOG00000012594
• Aliases: None
• Description: None

Sequence

>retro_cpor_1060
AAACACGGCTTCATGGTGCATAAAGGACGACCAGGCAAAATAGTGGAGATGTCAGTTCTGCAACTGGAAAGCAAGGTCGT
GCCAAAGTACACCTTGTTGGAACTGATATTTTCACAGGGAGAAAACATGAATGTGGTTGCCCTTTTACTTGCGACAAGGA
TGTTCCCAGTGAAAGAAATGATTATCAGCAGATATGCATTCAGGATGGTTACCTTTCCCTGCTCACCCAGACAGCGAAAT
CTGTGAGGGTCTCTTAACTGCCTGAAGGTGAACTAGGCAAAGAAATAGAAGGAAAACACAATGCAGGGGACAGGTAGAGA
TGTCTATCTTGTGAGCCATGAGTGAAGAGCAGGCTGTAGCCATAAAG

Alignment

ORF - retro_cpor_1060 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.46 %
• Parental protein coverage: 81.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KNGFVVLKGRPCKIVEMS-TSKTGKHGHAKVHLVGIDIFTGKKYEDICPSTHNMDVPNIKRNDYQLICIQ
          K.GF.V.KGRP.KIVEMS..S.TGK.G.AKVHLVG.DIFTG.K.E..CP.T...DVP...RNDYQ.ICIQ
Retrocopy KHGFMVHKGRPGKIVEMS<SSATGKQGRAKVHLVGTDIFTGRKHECGCPFTCDKDVPS-ERNDYQQICIQ

Parental  DGYLSLLTETGEVREDLKLPEGELGKEIEGKYNAGE-DVQVSVMCAMSEEYAVAIK
          DGYLSLLT.T........LPEGELGKEIEGK.NAG...V..S...AMSEE.AVAIK
Retrocopy DGYLSLLTQTAKSVRVS*LPEGELGKEIEGKHNAGD<QVEMSIL*AMSEEQAVAIK

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	4.95 RPM
SRP017611_kidney	0.00 RPM	2.83 RPM
SRP017611_liver	0.00 RPM	2.00 RPM
SRP040447_lung	0.00 RPM	1.21 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.90 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1060 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1060 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 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005363	1 retrocopy	retro_chof_1016,
Cavia porcellus	ENSCPOG00000012594	1 retrocopy	retro_cpor_1060 ,
Dasypus novemcinctus	ENSDNOG00000014801	2 retrocopies	retro_dnov_1133, retro_dnov_268,
Homo sapiens	ENSG00000163577	1 retrocopy	retro_hsap_1591,
Loxodonta africana	ENSLAFG00000013225	1 retrocopy	retro_lafr_901,
Macropus eugenii	ENSMEUG00000007473	2 retrocopies	retro_meug_1619, retro_meug_641,
Macaca mulatta	ENSMMUG00000022880	1 retrocopy	retro_mmul_2222,
Nomascus leucogenys	ENSNLEG00000005292	1 retrocopy	retro_nleu_1762,
Oryctolagus cuniculus	ENSOCUG00000016657	1 retrocopy	retro_ocun_65,
Pongo abelii	ENSPPYG00000014294	2 retrocopies	retro_pabe_1308, retro_pabe_1640,
Pan troglodytes	ENSPTRG00000015621	1 retrocopy	retro_ptro_1070,
Ictidomys tridecemlineatus	ENSSTOG00000008130	2 retrocopies	retro_itri_1400, retro_itri_689,
Tupaia belangeri	ENSTBEG00000000408	2 retrocopies	retro_tbel_1442, retro_tbel_4419,