RetrogeneDB ID: retro_cpor_815

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_29:15983444..15983838(-)
• Located in intron of: ENSCPOG00000009240

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGH
• Ensembl ID: ENSCPOG00000003328
• Aliases: None
• Description: None

Sequence

>retro_cpor_815
GGCTTGTACACCATTGTTACCTGTACTCAGTGAGCCTCGACTCCCATTTTTGTCACCCTCTTAAGCGTGCTTGCTTATCT
TCATCAGGTAAAGACTACTCAGGAGACTGTTAAATCACTGATTCCTTTGTCATCTGGACAACTTCGCCCTATGCTTCAGG
TAAAGAAAGCACTACCTTCACAGAGATGGGCAAGGTGAAGGATACTGTGATTAACAGACTATTTACATGCAGAAGGTGAT
TAATTACTTCTGAAATTTACTGAAGGATCCAGTGGAACCACACAGTATATCCCAAATAGCACCTATGTTTCAAAGTACTA
AGACCCCGGAAAACTGCCTGACAGGAGAAGGCAACAGCTGTCAGGAGGGCCTGATACAAGGACGCCACATCACC

Alignment

ORF - retro_cpor_815 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.73 %
• Parental protein coverage: 70.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GLFTLCENSTILSAAIFITVLGLLGYLHFVKIDQETLL-IIDSLGIQMTSSYASGKENTTFIEMDKVKDI
          GL.T........S..IF.T.L..L.YLH.VK..QET...I.DS..I..TS.YASGKE.TTF.EM.KVKD.
Retrocopy GLYTIVTCTQ*ASTPIFVTLLSVLAYLHQVKTTQETVK<ITDSFVIWTTSPYASGKESTTFTEMGKVKDT

Parental  VIN-EAIYMQKVIYYLCILLKDPREPQKISQVVPVFQSAKPRLDCLIEVYKSCQEVLAHQKATT
          VIN...IYMQKVI.Y...LLKDP.EP..ISQ..P.FQS.K....CL.....SCQE.L......T
Retrocopy VIN<QTIYMQKVINYF*NLLKDPVEPHSISQIAPMFQSTKTPENCLTGEGNSCQEGLIQGRHIT

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	10.30 RPM
SRP017611_kidney	0.10 RPM	7.33 RPM
SRP017611_liver	0.04 RPM	1.96 RPM
SRP040447_lung	0.00 RPM	3.68 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.06 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_815 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_815 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003328	1 retrocopy	retro_cpor_815 ,
Echinops telfairi	ENSETEG00000008623	1 retrocopy	retro_etel_844,
Homo sapiens	ENSG00000100564	1 retrocopy	retro_hsap_1506,
Gorilla gorilla	ENSGGOG00000001507	1 retrocopy	retro_ggor_1155,
Macropus eugenii	ENSMEUG00000011325	1 retrocopy	retro_meug_2130,
Myotis lucifugus	ENSMLUG00000004467	1 retrocopy	retro_mluc_910,
Nomascus leucogenys	ENSNLEG00000000739	1 retrocopy	retro_nleu_1747,
Pongo abelii	ENSPPYG00000005925	1 retrocopy	retro_pabe_1255,
Pan troglodytes	ENSPTRG00000006466	1 retrocopy	retro_ptro_1020,
Tarsius syrichta	ENSTSYG00000008465	1 retrocopy	retro_tsyr_1926,