RetrogeneDB ID: retro_cpor_136

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_0:64495081..64495497(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL10
• Ensembl ID: ENSCPOG00000001642
• Aliases: None
• Description: None

Sequence

>retro_cpor_136
GAGCTTGAGCAGTACCAGTTGCTGGTGCTAGCTCTGCATGGCTACGAAAGGGCACATTCCTGAGCCAGCTGTTGGGGAAG
CCACCGCTGGAAGACCCCATTTCCACCTGGAGCTTCAACTCCATGCGGCTGCCCCCCGAAGATTTTGAGGTGGACCTTGT
AGAAATAGGTGACAGCTAAAACCTCTGCTTCTACAGGAAGGAGTCTGTGAATGGAGTGGATGTATTCGTGTTCATGATGG
GCTCAGCTGACTGGCTGTGGCTGCCCTGGGCTGGACAGGAACTGCACAAGCTGCTAGACAAGGACCCCGACCTGCCTGGC
TAACAGGTGGCTAACAGGCAGGACCTGAGCGAGGCTGAGAGTGTGGGGGAGCTGCAGCAGGAGGTGGGCCTGCAGGTTCC
TGACAGCCAGCCGGAG

Alignment

ORF - retro_cpor_136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.86 %
• Parental protein coverage: 56.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELEQREVLVLGLDG-CGKSTFLRVLSGKTPLEGHVPTWGFNSVRLPTKDFEVDLLEIGGSQNLRFYWKEF
          ELEQ...LVL.L.G...K.TFL..L.GK.PLE....TW.FNS.RLP..DFEVDL.EIG.S.NL.FY.KE.
Retrocopy ELEQYQLLVLALHG<LRKGTFLSQLLGKPPLEDPISTWSFNSMRLPPEDFEVDLVEIGDS*NLCFYRKES

Parental  VNEVDVLVFMVDSADRLRLPWARQELHKLLDKDPDLPVVVVANKQDLSEAMSVVELQQELGLQAIDNQRE
          VN.VDV.VFM..SAD.L.LPWA.QELHKLLDKDPDLP...VAN.QDLSEA.SV.ELQQE.GLQ..D.Q.E
Retrocopy VNGVDVFVFMMGSADWLWLPWAGQELHKLLDKDPDLPG*QVANRQDLSEAESVGELQQEVGLQVPDSQPE

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	3.57 RPM
SRP017611_kidney	0.00 RPM	1.15 RPM
SRP017611_liver	0.00 RPM	0.96 RPM
SRP040447_lung	0.03 RPM	2.72 RPM
SRP040447_skeletal_muscle	0.00 RPM	23.69 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_136 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_136 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001642	3 retrocopies	retro_cpor_136 , retro_cpor_1479, retro_cpor_933,
Dasypus novemcinctus	ENSDNOG00000002678	1 retrocopy	retro_dnov_2004,
Oryctolagus cuniculus	ENSOCUG00000016961	1 retrocopy	retro_ocun_219,