RetrogeneDB ID: retro_cpor_176

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:37749061..37749264(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS28
• Ensembl ID: ENSCPOG00000022876
• Aliases: None
• Description: None

Sequence

>retro_cpor_176
ATGGACACAAGTCATTTGCAGCTCATTAAGCTGGCTAATGTCACCAAAGTGCTGGGCAGGCCTGGCTCACAAGGACAGTG
CAAACAGTTGCTTGGGGAATTCATGGACGACGTGAGCCTCGCCATCATCCACAAAGTGAAAGAGTCCATGCATGAGGGTG
AGCTGCTCATCCTGTTGAATCAGAGTGGGAACCCAGGAGGTTG

Alignment

ORF - retro_cpor_176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.22 %
• Parental protein coverage: 98.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLL-ESEREARRL
          MDTS..Q.IKLA.VTKVLGR.GSQGQC.Q...EFMDD.S..II..VK....EG..L.LL.ESE.E.RRL
Retrocopy MDTSHLQLIKLANVTKVLGRPGSQGQCKQLLGEFMDDVSLAIIHKVKESMHEGELLILL<ESEWEPRRL

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	35.83 RPM
SRP017611_kidney	0.00 RPM	75.37 RPM
SRP017611_liver	0.00 RPM	48.10 RPM
SRP040447_lung	0.00 RPM	240.20 RPM
SRP040447_skeletal_muscle	0.00 RPM	248.20 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_176 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_176 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 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004917	1 retrocopy	retro_amel_1359,
Bos taurus	ENSBTAG00000002468	1 retrocopy	retro_btau_1130,
Cavia porcellus	ENSCPOG00000022876	5 retrocopies	retro_cpor_1092, retro_cpor_1485, retro_cpor_1504, retro_cpor_176 , retro_cpor_702,
Equus caballus	ENSECAG00000017256	1 retrocopy	retro_ecab_725,
Loxodonta africana	ENSLAFG00000029923	2 retrocopies	retro_lafr_168, retro_lafr_755,
Myotis lucifugus	ENSMLUG00000023621	1 retrocopy	retro_mluc_2040,
Macaca mulatta	ENSMMUG00000028895	3 retrocopies	retro_mmul_122, retro_mmul_182, retro_mmul_807,
Monodelphis domestica	ENSMODG00000003890	1 retrocopy	retro_mdom_291,
Mus musculus	ENSMUSG00000067288	3 retrocopies	retro_mmus_2949, retro_mmus_3283, retro_mmus_91,
Rattus norvegicus	ENSRNOG00000042886	2 retrocopies	retro_rnor_95, retro_rnor_96,