RetrogeneDB ID: retro_cpor_1479

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_9:42306763..42307220(+)
• 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_1479
GGGAACAGCGCGTTCTCTACGTGCTGTCGCGGAAGACTCCCCTGGAAGGCCGCGTCCCCACTTGGGACTTCAACTCTGTG
CGGCTGCCCACCAAAGACTTCGAGATGGACCTTCCAGAGATTGGTAGCAGCCAGAACTTGCACTTCTACTGGAAGGAGTT
GGGAATGAGGTAGTGTACTAATGTTCATGGTAAACTCAGCTGACTGGCTCTGGCTACCTTAGGCCTGACAGGAACTGCAC
AAGCTGTTAGACAAGGACCCCAGCCTGCCTGTCGTAGTGGTGGCCAACAAGCGGAACCTGAGCAAGGCCATGAGTGTGAC
GGAGCTGCAGCGGGACCTGGGCCTGCAGGCTGCCAGCGGGAGGTTTTTCTTTTGGCAGCCAGCATTCCCTTGCAGGATCT
GGCTTTGAAGAACCTGGCACCGTGCACATCTGGAAACTACTCTTGGACCTTCTTTCC

Alignment

ORF - retro_cpor_1479 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.53 %
• Parental protein coverage: 63.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GKSTF-LRVLSGKTPLEGHVPTWGFNSVRLPTKDFEVDLLEIGGSQNLRFYWKEFV-NEV-DVLVFMVDS
          G.S.F.L.VLS.KTPLEG.VPTW.FNSVRLPTKDFE.DL.EIG.SQNL.FYWKE...NEV..VL.FMV.S
Retrocopy GNSAF<LYVLSRKTPLEGRVPTWDFNSVRLPTKDFEMDLPEIGSSQNLHFYWKELG<NEV<SVLMFMVNS

Parental  ADRLRLPWARQELHKLLDKDPDLPVVVVANKQDLSEAMSVVELQQELGLQAIDNQREIFF-LAASI-APA
          AD.L.LP.A.QELHKLLDKDP.LPVVVVANK..LS.AMSV.ELQ..LGLQA.......FF.LAASI...A
Retrocopy ADWLWLP*A*QELHKLLDKDPSLPVVVVANKRNLSKAMSVTELQRDLGLQAASGR--FFF<LAASI<SLA

Parental  GSGFEEPGTVHIWKLLLELLS
          GSGFEEPGTVHIWKLLL.LLS
Retrocopy GSGFEEPGTVHIWKLLLDLLS

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	0.05 RPM	2.72 RPM
SRP040447_skeletal_muscle	0.01 RPM	23.69 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1479 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1479 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,