RetrogeneDB ID: retro_cpor_98

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:38772468..38772684(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000008681
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000008678
• Aliases: None
• Description: None

Sequence

>retro_cpor_98
ATGGTGCCACCAGTGCAGGTCTCTCCGCTCATCAAGCTCGGCCGCTACTCTGCCCTGGTTGTTGGCATCGCCTACGGAGC
CAAGCGTTATAGTTACCTGAAGCCTCGGGCAGAGGAAGAAAGGCGGGTAGCCGAAGAGGAGAAGAAGAGGCAGGATGAGT
TGAAACGAATCGAGAGGGAACTGGCAGAAGCCCGGGATGACAGTATACTGAAGTGA

Alignment

ORF - retro_cpor_98 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVPPVQVSPLIKLGRYSALVVGIAYGAKRYSYLKPRAEEERRVAEEEKKRQDELKRIERELAEAQDDSIL
          MVPPVQVSPLIKLGRYSALVVGIAYGAKRYSYLKPRAEEERRVAEEEKKRQDELKRIERELAEA.DDSIL
Retrocopy MVPPVQVSPLIKLGRYSALVVGIAYGAKRYSYLKPRAEEERRVAEEEKKRQDELKRIERELAEARDDSIL

Parental  K
          K
Retrocopy K

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	0.35 RPM	39.74 RPM
SRP017611_kidney	0.31 RPM	85.53 RPM
SRP017611_liver	0.04 RPM	47.84 RPM
SRP040447_lung	0.10 RPM	22.42 RPM
SRP040447_skeletal_muscle	0.47 RPM	112.52 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_98 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_98 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016722	2 retrocopies	retro_amel_1171, retro_amel_1761,
Bos taurus	ENSBTAG00000017496	2 retrocopies	retro_btau_1222, retro_btau_219,
Canis familiaris	ENSCAFG00000023527	1 retrocopy	retro_cfam_62,
Callithrix jacchus	ENSCJAG00000001989	1 retrocopy	retro_cjac_352,
Cavia porcellus	ENSCPOG00000008678	1 retrocopy	retro_cpor_98 ,
Felis catus	ENSFCAG00000029708	1 retrocopy	retro_fcat_268,
Mustela putorius furo	ENSMPUG00000011414	1 retrocopy	retro_mputfur_494,
Mus musculus	ENSMUSG00000050856	1 retrocopy	retro_mmus_3152,
Otolemur garnettii	ENSOGAG00000012271	1 retrocopy	retro_ogar_1292,
Rattus norvegicus	ENSRNOG00000000064	1 retrocopy	retro_rnor_697,
Tursiops truncatus	ENSTTRG00000002962	1 retrocopy	retro_ttru_1938,