RetrogeneDB ID: retro_cpor_119

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_23:31617280..31617556(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000026063
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000013370
• Aliases: None
• Description: None

Sequence

>retro_cpor_119
ATGACTTCTACACTGGCCCAGGGGCTGGGGCGAATCACAGACCAGCTGGGCTACCTGGTACTGAGTGAAGGTGCAGCACT
GGCATCACCTGGGAATCTCAAGAGTGATGAACAGGCAGCCAGTGCCATCTCTGAGCTGGTCAGCACAGCTTGTGGCTTCC
AGCTGCACCACGGCATGGATGTCCCCTTCAATCACCTGTCTGTGGTCTTTAGAGAACACACGCTGCTGGTGACTGTGTCA
GGACAGAGTGGGTTTGTGGTGAAGAGGCAGAACTGA

Alignment

ORF - retro_cpor_119 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.22 %
• Parental protein coverage: 91.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHHGMTVPFKRLSVVFG
          TS.L.QGL.RI.DQLGYLVLSEGA.LAS.G.L..DEQAASAISELVSTACGF.LHHGM.VPF..LSVVF.
Retrocopy TSTLAQGLGRITDQLGYLVLSEGAALASPGNLKSDEQAASAISELVSTACGFQLHHGMDVPFNHLSVVFR

Parental  EHTLLVTVSGQRVFVVKRQN
          EHTLLVTVSGQ..FVVKRQN
Retrocopy EHTLLVTVSGQSGFVVKRQN

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	8.74 RPM
SRP017611_kidney	0.00 RPM	35.80 RPM
SRP017611_liver	0.00 RPM	16.89 RPM
SRP040447_lung	0.00 RPM	26.63 RPM
SRP040447_skeletal_muscle	0.00 RPM	19.47 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_119 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_119 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014561	1 retrocopy	retro_cfam_1491,
Cavia porcellus	ENSCPOG00000013370	1 retrocopy	retro_cpor_119 ,
Mus musculus	ENSMUSG00000050552	1 retrocopy	retro_mmus_3544,
Ochotona princeps	ENSOPRG00000003476	1 retrocopy	retro_opri_640,
Pteropus vampyrus	ENSPVAG00000011987	1 retrocopy	retro_pvam_1449,