RetrogeneDB ID: retro_cpor_28

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_22:18979711..18980221(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000023849
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000008258
• Aliases: None
• Description: None

Sequence

>retro_cpor_28
TCTGCTAAATCGAAAAATAAAAATCTTAAACCTGGTCCTAAGAATGCTAAACAGAAGAAAGTGAAAGGAAAACGGGCTGG
CACTGGAGACAGAGGGCCAGATTCCTTGGTGAAGAAGAGCAGTCCCGGGGAGGAGGATGGTGAACCTAAGGAGAAGCAGC
AGCCGGTGCGGATGAGCCAGGGCTTCATTAACCAGCACACAGTGGAACGTAAGGGCAAGAAAGTTTGCAAATATTTTTTT
GAAAGGAAATGTATCAAGGGAGACCAGTGTACGTTTGATCATGATACAGAGATGGAGAAAAAAAAGGAAATGTGTAAGTT
TTATGTCCAGGGCTATTTTACCCGAGGTGAAAACTGCCTGTATTTGCATAATGAATACCCCTGCAAGTTTTATCACACAG
GAACAAAATGTTACCAGGGAGAGCACTGCAGGTTTTCCCATGCTCCCCTGACGGCCAAAACACAGGAGCTGTTGGCTAAA
GTTTTGGATACCGAAAAGAAGACATGTAAA

Alignment

ORF - retro_cpor_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.08 %
• Parental protein coverage: 55.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SAKSKNTNLKPGRKNAKQKKVKRKRAGTGDRGPDSLLKKSSPQDEDGEPKEKQQPVRMSQGFINQHTVER
          SAKSKN.NLKPG.KNAKQKKVK.KRAGTGDRGPDSL.KKSSP..EDGEPKEKQQPVRMSQGFINQHTVER
Retrocopy SAKSKNKNLKPGPKNAKQKKVKGKRAGTGDRGPDSLVKKSSPGEEDGEPKEKQQPVRMSQGFINQHTVER

Parental  KGKKVCKYFLERKCIKGDQCKFDHDTEMEKKKEMCKFYVQGYCTRGENCLYLHNEYPCKFYHTGTKCYQG
          KGKKVCKYF.ERKCIKGDQC.FDHDTEMEKKKEMCKFYVQGY.TRGENCLYLHNEYPCKFYHTGTKCYQG
Retrocopy KGKKVCKYFFERKCIKGDQCTFDHDTEMEKKKEMCKFYVQGYFTRGENCLYLHNEYPCKFYHTGTKCYQG

Parental  EHCRFSHAPLTAETQELLAKVLDTEKKTC
          EHCRFSHAPLTA.TQELLAKVLDTEKKTC
Retrocopy EHCRFSHAPLTAKTQELLAKVLDTEKKTC

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	0.23 RPM	2.13 RPM
SRP017611_kidney	0.10 RPM	5.02 RPM
SRP017611_liver	0.22 RPM	1.52 RPM
SRP040447_lung	0.05 RPM	1.29 RPM
SRP040447_skeletal_muscle	0.28 RPM	2.44 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_28 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_28 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008258	1 retrocopy	retro_cpor_28 ,
Dasypus novemcinctus	ENSDNOG00000018056	1 retrocopy	retro_dnov_1975,
Oryctolagus cuniculus	ENSOCUG00000011253	1 retrocopy	retro_ocun_1773,
Otolemur garnettii	ENSOGAG00000002554	2 retrocopies	retro_ogar_1723, retro_ogar_2745,