RetrogeneDB ID: retro_cpor_524

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_18:13710742..13711714(-)
• Located in intron of: ENSCPOG00000013915

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000021865
• Aliases: None
• Description: None

Sequence

>retro_cpor_524
CTACTTCGTGTACTGCTGCAGAGTGGGGCTCCAGCTATGCCCCAGCTGTTGCACATGCCAGACTTTGAGGGACTGTACCC
AGTGCACCTAGCAGTTCGTGCCCGGAGCCCTGAGTGCCTGGACCTGCTGGTGGATAGTGGTGCTGATGTGGAGGCTGCCG
AGCGACAGGGTGGCCGCACAGCCCTGCATCTGGCCACAGAGATGGAGGAGCTGGGGTTGGTCACCCACCTGGTTACCAAG
CTGCATGCCAATGTGAATGCCCGAACCTTTGCTGGAAACACACCCCTACACCTGGCAGCTGGACTGGGTTCCCCAACCCT
CACCCGCCTCCTCCTGAAGGCTGGGGCTGACATCCACGCAGAGAATGAGGAGCCCCTGTGCCCATTGTCTTCACCCCCCA
CCTCTGGGAGTGACTCGGATTCTGAGGGTCCTGAGAGGGATGCCAGAGGCAGCTTCCAGGGCCACACACCACTTGATCTC
ACTCGGAGCACTAAGGTGAAGACCTTGCTGCTTAATGCTGCTCAGACCTCCTCGGAGCCCCCGAACATCCCACCCAGCCC
TGCAGGGCCAGGGCTGTCCCTGGGTGAGACCACCCTACAAAACCTGGAGCAGCTGCTAGATGGGCCAGAAGCTCAGGGCA
GCTGGGCAGAGCTGGCTGAGCGACTGGGCTTACGCAGTCTGGTGGACACGTATCGGAAGACCCCCTCACCCAGTGGCAGC
CTCCTGCGCAGCTACAAGCTGGCTGGTGGGGACCTGGCAGGTCTGCTGGACGCACTGTCTGCCATGGGTCTAGATGAGGG
GGTGAAACTGCTGAGAGGTCCAGAGACCAGAGACAAACTGCCCAGTACAGCTGAAGTGAAGGAAGACAGTGCCTATGGCA
GCCAGTCCGTGGAACAGGAGGCAGAGACACTGGGCCCACTCCCTGAGCCCCCCGGGGGCCTCTGCCATGGGCACCCTCAG
CCTCAGGTGCAC

Alignment

ORF - retro_cpor_524 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.69 %
• Parental protein coverage: 70.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLRVLLQSGAPAMPQLLHMPDFEGLYPVHLAVRARSPECLDLLVDSGADVEAAERQGGRTALHLATEMEE
          LLRVLLQSGAPAMPQLLHMPDFEGLYPVHLAVRARSPECLDLLVDSGADVEAAERQGGRTALHLATEMEE
Retrocopy LLRVLLQSGAPAMPQLLHMPDFEGLYPVHLAVRARSPECLDLLVDSGADVEAAERQGGRTALHLATEMEE

Parental  LGLVTHLVTKLHANVNARTFAGNTPLHLAAGLGSPTLTRLLLKAGADIHAENEEPLCPLSSPPTSGSDSD
          LGLVTHLVTKLHANVNARTFAGNTPLHLAAGLGSPTLTRLLLKAGADIHAENEEPLCPLSSPPTSGSDSD
Retrocopy LGLVTHLVTKLHANVNARTFAGNTPLHLAAGLGSPTLTRLLLKAGADIHAENEEPLCPLSSPPTSGSDSD

Parental  SEGPERDARGSFQGHTPLDLTRSTKVKTLLLNAAQTSSEPPNIPPSPAGPGLSLGETTLQNLEQLLDGPE
          SEGPERDARGSFQGHTPLDLTRSTKVKTLLLNAAQTSSEPPNIPPSPAGPGLSLGETTLQNLEQLLDGPE
Retrocopy SEGPERDARGSFQGHTPLDLTRSTKVKTLLLNAAQTSSEPPNIPPSPAGPGLSLGETTLQNLEQLLDGPE

Parental  AQGSWAELAERLGLRSLVDTYRKTPSPSGSLLRSYKLAGGDLAGLLDALSAMGLDEG-KLLRGPETRDKL
          AQGSWAELAERLGLRSLVDTYRKTPSPSGSLLRSYKLAGGDLAGLLDALSAMGLDEG.KLLRGPETRDKL
Retrocopy AQGSWAELAERLGLRSLVDTYRKTPSPSGSLLRSYKLAGGDLAGLLDALSAMGLDEGVKLLRGPETRDKL

Parental  PSTAEVKEDSAYGSQSVEQEAETLGPLPEPPGGLCHGHPQPQVH
          PSTAEVKEDSAYGSQSVEQEAETLGPLPEPPGGLCHGHPQPQVH
Retrocopy PSTAEVKEDSAYGSQSVEQEAETLGPLPEPPGGLCHGHPQPQVH

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	0.40 RPM	4.37 RPM
SRP017611_kidney	1.99 RPM	32.35 RPM
SRP017611_liver	0.65 RPM	6.92 RPM
SRP040447_lung	2.67 RPM	58.94 RPM
SRP040447_skeletal_muscle	0.92 RPM	15.67 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_524 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_524 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000021865	1 retrocopy	retro_cpor_524 ,