RetrogeneDB ID: retro_cpor_34

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_27:21539993..21540392(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000002243
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000014056
• Aliases: None
• Description: None

Sequence

>retro_cpor_34
ATGGTGGAGGCTTTCTGTGCTACTTGGAAGCTGACGGACACTCAGAACTTTGACGAGTACATGAAGGCCCTAGGCCTGGG
CTTTGCCACGAGGCAGGTGGGGAACGTGACCAAGCCCACAGTGATTATTAGTCAGGAGGCCGGCCGGGTGGTGATCAGGA
CCCAGTGCACGTTCAAGAACACGGAGATCAGCTTCTTTCTGGGGGAGGAGTTTGACGAAATCAGTGTGGACGACCGAAAG
TGTAAGTCTGTTGTTAGCCTGGACGGAGGCAAACTTGTGCACATACAGAAATGGGACGGCAAGGAGATGAAGTTTGTGAG
AGAAATTAAAGATGACAAAATGGTTAGGACTCTGACTTTTGGTGACGTTGTCTGTGTTCGCCAGTATGAGAAAGTGTAA

Alignment

ORF - retro_cpor_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVEAFCATWKLTDSQNFDEYMKALGVGFATRQVGNVTKPTVIISQEAGRVVIRTQCTFKNTEISFFLGEE
          MVEAFCATWKLTD.QNFDEYMKALG.GFATRQVGNVTKPTVIISQEAGRVVIRTQCTFKNTEISFFLGEE
Retrocopy MVEAFCATWKLTDTQNFDEYMKALGLGFATRQVGNVTKPTVIISQEAGRVVIRTQCTFKNTEISFFLGEE

Parental  FDEISVDDRKCKSVVSLDGGKLVHIQKWDGKETKFVREIKDDKMVMTLTFGDVVCVRQYEKV
          FDEISVDDRKCKSVVSLDGGKLVHIQKWDGKE.KFVREIKDDKMV.TLTFGDVVCVRQYEKV
Retrocopy FDEISVDDRKCKSVVSLDGGKLVHIQKWDGKEMKFVREIKDDKMVRTLTFGDVVCVRQYEKV

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	23.35 RPM
SRP017611_kidney	0.00 RPM	2.83 RPM
SRP017611_liver	0.00 RPM	3.96 RPM
SRP040447_lung	0.00 RPM	0.03 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.04 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_34 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_34 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014056	1 retrocopy	retro_cpor_34 ,
Cavia porcellus	ENSCPOG00000025732	1 retrocopy	retro_cpor_948,
Homo sapiens	ENSG00000164434	1 retrocopy	retro_hsap_536,
Gorilla gorilla	ENSGGOG00000025475	1 retrocopy	retro_ggor_489,
Macaca mulatta	ENSMMUG00000021907	1 retrocopy	retro_mmul_458,
Oryctolagus cuniculus	ENSOCUG00000001497	1 retrocopy	retro_ocun_1874,
Otolemur garnettii	ENSOGAG00000031110	1 retrocopy	retro_ogar_2821,
Ochotona princeps	ENSOPRG00000000992	1 retrocopy	retro_opri_840,
Pongo abelii	ENSPPYG00000016979	1 retrocopy	retro_pabe_213,
Pan troglodytes	ENSPTRG00000018564	1 retrocopy	retro_ptro_402,
Sarcophilus harrisii	ENSSHAG00000003313	1 retrocopy	retro_shar_521,