RetrogeneDB ID: retro_cpor_775

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_27:14747477..14747918(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRR3
• Ensembl ID: ENSCPOG00000022770
• Aliases: None
• Description: None

Sequence

>retro_cpor_775
CCCCCACTGCCTGAGTGGAAAGAGACTGGAGATGAGGAAAATGAGAATCCCACCAGACCACACAGCCGTCTAGGTCTGCA
CCCCACGGCCAATGGAAAGCCTGCTGACCCCAAAGTCCGCTCTTCAGAGAGGTCCGCCAGGACCAGCAGGACCAATGATC
CCATCAATGCTGAGTCTTCCATCTCCTCCCAGTGGGAGTGACCTAATTAAGAGAGGCCTTGGCCCCAGGCCCACCCTATA
TGTTCATGGTTGATGGGAAAGTCAGTGCTGAGCCTCTGTTTCTACAGCTAAACCATAGGAATCCCTCCGGGGAAAGCTTT
CAGGAAGAGCTGAGAACCCTCAAGGACTCTAAAGCTGGTCTCCTATCAGGATTACCTGAGTACCTAAAGGTGCCCTCAGG
TGAGAGAAGACAAATCTAACTGCCTTGTTTGCCAGTACTTT

Alignment

ORF - retro_cpor_775 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.66 %
• Parental protein coverage: 78.49 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PTLPDREETGDEE-ESPIGPPSLLGPPPMANGEPGDPT-PAFRRGPPGSRRLRIPPLLSLPPPPRGRGPF
          P.LP...ETGDEE.E.P..P.S.LG..P.ANG.P.DP...A..RGPPG.....IP..LSLP.PP.G....
Retrocopy PPLPEWKETGDEENENPTRPHSRLGLHPTANGKPADPK>SALQRGPPGPAGPMIPSMLSLPSPPSGSDLI

Parental  RGGLGPRTGPYGRGWWG-VNAEPLFRGPGHRGPPRESFYKE-QTNPRRLRSWSLAKRTCPPKDS-PQVVE
          ..GLGPR...Y..G.W..V.AEPLF....HR.P..ESF..E...NP..L.SWS....T..PK...PQV.E
Retrocopy KRGLGPRPTLYVHG*WE>VSAEPLFLQLNHRNPSGESFQEE<AENPQGL*SWSPIRIT*VPKGA<PQVRE

Parental  DKSNRPVCRHF
          DKSN..VC..F
Retrocopy DKSNCLVCQYF

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	7.71 RPM
SRP017611_kidney	0.00 RPM	10.36 RPM
SRP017611_liver	0.00 RPM	3.18 RPM
SRP040447_lung	0.00 RPM	10.26 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.57 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_775 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_775 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000022770	1 retrocopy	retro_cpor_775 ,
Felis catus	ENSFCAG00000025918	2 retrocopies	retro_fcat_1094, retro_fcat_1698,
Gorilla gorilla	ENSGGOG00000014604	1 retrocopy	retro_ggor_1915,
Myotis lucifugus	ENSMLUG00000008758	1 retrocopy	retro_mluc_1567,
Macaca mulatta	ENSMMUG00000013893	1 retrocopy	retro_mmul_1431,
Nomascus leucogenys	ENSNLEG00000005104	1 retrocopy	retro_nleu_1548,
Otolemur garnettii	ENSOGAG00000004430	2 retrocopies	retro_ogar_1030, retro_ogar_1324,
Pongo abelii	ENSPPYG00000016409	1 retrocopy	retro_pabe_2279,
Pan troglodytes	ENSPTRG00000017929	1 retrocopy	retro_ptro_1861,
Sorex araneus	ENSSARG00000002747	2 retrocopies	retro_sara_143, retro_sara_9,
Ictidomys tridecemlineatus	ENSSTOG00000011829	1 retrocopy	retro_itri_126,
Tarsius syrichta	ENSTSYG00000000166	2 retrocopies	retro_tsyr_308, retro_tsyr_841,