RetrogeneDB ID: retro_cpor_615

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_20:1480975..1481692(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000026779
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPA1
• Ensembl ID: ENSCPOG00000014023
• Aliases: None
• Description: None

Sequence

>retro_cpor_615
GTTCCACACTGGTCTAATGCAAAAGTGGAGTTCTCTACACAGGACCCTTTAAATCAAATTAAGCAAGATGTAAAAAGGGG
AAACTCTGTTATGTTGCAAATTTGTTCCCTCATAAAGGATGTATCTGGAACTATGGTGCCATCTCTCAGACTTGGGAAGA
CCCAGGACACTTTGACAAACATACTGGCTATGATGGTGACAATGACCCAATTGATGTTTGTGAAATCGAAAGCAAGGTGT
GTGCAAGAGGTGGAATAATCAGGTGAAAGTTCGAGGCACCTTGGCTAGCACTGACGAAGAAGAAACCGACCGGAAAATCA
TTGCCATTAAAGTGGACGGTCCTGAGGCAGCCAGTTATAATGGTATCAATGACGTTGAACGGCTGACACCTGGCTACCGA
GAAGCTACTGTGGACTGGTTTAGAAGGTACAAGGTTCCTGATGGGAAACCAGAAAACAAATTTGCTTTGAATGCAGAATT
GAAAGATAAGGACTTTGCAGTTGGTATCATTAAAAGCACTCTTGACTATTGGAAAGCATTAGTGATTAACAACATGAACA
GGAAAGGAATCAGTTGCATGAACACAGCAGTGTCTGAGACTCCTTTCAAGTGTGACCCTGATGCTGCCAAAGCTATCATG
GACGTGTTACTCCTGCCATGTGATCTGCCTACACAGTACCAACAGGTGTGGACAAGCGGTGCCATCACCAGAAAAAC

Alignment

ORF - retro_cpor_615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 83.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VPRWSNAKMEIATKDPLNPIKQDVK-KGKLRYVANLFPYKGYIWNYGAIPQTWEDPGHSDKHTGCCGDND
          VP.WSNAK.E..T.DPLN.IKQDVK.KGKL.YVANLFP.KG.IWNYGAI.QTWEDPGH.DKHTG..GDND
Retrocopy VPHWSNAKVEFSTQDPLNQIKQDVK<KGKLCYVANLFPHKGCIWNYGAISQTWEDPGHFDKHTGYDGDND

Parental  PIDVCEIGSKVCARGEIIR-VKVLGILAMIDEGETDWKVIAINVDDPDAANYNDINDVERLKPGYLEATV
          PIDVCEI.SKVCARG.IIR.VKV.G.LA..DE.ETD.K.IAI.VD.P.AA.YN.INDVERL.PGY.EATV
Retrocopy PIDVCEIESKVCARGGIIR<VKVRGTLASTDEEETDRKIIAIKVDGPEAASYNGINDVERLTPGYREATV

Parental  DWFRRYKVPDGKPENQFAFNAEFKDKNFAVDIIKSTHDYWKALVTKKTDGKGISCMNTTVSESPFKCDPD
          DWFRRYKVPDGKPEN.FA.NAE.KDK.FAV.IIKST.DYWKALV......KGISCMNT.VSE.PFKCDPD
Retrocopy DWFRRYKVPDGKPENKFALNAELKDKDFAVGIIKSTLDYWKALVINNMNRKGISCMNTAVSETPFKCDPD

Parental  AAKAIVDALPPPCD-SAHTVPTEVDKWFHHQKN
          AAKAI.D.L..PCD.SA.TVPT.VDK..HHQKN
Retrocopy AAKAIMDVLLLPCD<SAYTVPTGVDKRCHHQKN

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	0.06 RPM	72.76 RPM
SRP017611_kidney	0.00 RPM	40.30 RPM
SRP017611_liver	0.00 RPM	63.64 RPM
SRP040447_lung	0.00 RPM	78.24 RPM
SRP040447_skeletal_muscle	0.00 RPM	53.73 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_615 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_615 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014023	1 retrocopy	retro_cpor_615 ,
Homo sapiens	ENSG00000180817	2 retrocopies	retro_hsap_2756, retro_hsap_3267,
Loxodonta africana	ENSLAFG00000004048	1 retrocopy	retro_lafr_990,
Myotis lucifugus	ENSMLUG00000017790	1 retrocopy	retro_mluc_2469,
Macaca mulatta	ENSMMUG00000006397	1 retrocopy	retro_mmul_1540,
Nomascus leucogenys	ENSNLEG00000016098	1 retrocopy	retro_nleu_7,
Oryctolagus cuniculus	ENSOCUG00000016001	2 retrocopies	retro_ocun_1373, retro_ocun_883,
Procavia capensis	ENSPCAG00000006788	1 retrocopy	retro_pcap_247,
Pongo abelii	ENSPPYG00000029405	1 retrocopy	retro_pabe_37,
Pan troglodytes	ENSPTRG00000002585	2 retrocopies	retro_ptro_1864, retro_ptro_2210,
Tupaia belangeri	ENSTBEG00000008947	3 retrocopies	retro_tbel_3560, retro_tbel_3561, retro_tbel_848,
Tarsius syrichta	ENSTSYG00000005511	1 retrocopy	retro_tsyr_1856,