RetrogeneDB ID: retro_cpor_18

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_103:3705302..3705878(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000021968
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RAC3
• Ensembl ID: ENSCPOG00000013861
• Aliases: None
• Description: None

Sequence

>retro_cpor_18
ATGCAGAGCATCAAGTGTGTAGTGGTGGGTGATGGGGCTGTAGGCAAGACGTGTCTGCTCATCTGCTATACCACCAACGC
CTTCCCCAAAGAGTACATCCCCACAGTGTTCGACAATTACAGCGCCCAGAGTGCAGTTGACGGGCGCACAGTGAACCTGA
ACCTGTGGGACACTGCGGGCCAGGAGGAATATGACCGCCTCCGCACGCTCTCCTACCCTCAGACCAACGTCTTTGTCATC
TGTTTCTCTATTGCCAGTCCACCCTCCTATGAGAATGTGAGGCACAAGTGGCATCCAGAGGTGTGCCACCACTGCCCGGA
TGTGCCCATCCTTCTGGTGGGCACCAAGAAGGACCTGAGAGCCCAGCCTGATACCCTGCGGCGCCTCAAGGAGCAGGGCC
AGGCGCCCATCACACCACAGCAGGGCCAAGCACTGGCCAAGCAGATCCACGCTGTGCGCTACCTCGAGTGCTCGGCCCTA
CAGCAGGATGGCGTGAAGGAAGTGTTTGCCGAGGCTGTCCGGGCAGTGCTCAACCCTACACCGATCAAGCGCGGGCGGTC
CTGCGTCCTCTTGTGA

Alignment

ORF - retro_cpor_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.16 %
• Parental protein coverage: 99.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPL
          MQ.IKCVVVGDGAVGKTCLLI.YTTNAFP.EYIPTVFDNYSA...VDG..VNL.LWDTAGQE.YDRLR.L
Retrocopy MQSIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQSAVDGRTVNLNLWDTAGQEEYDRLRTL

Parental  SYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPHTPILLVGTKLDLRDDKDTIERLRDKKLAPITYP
          SYPQT.VF.ICFS..SP.S.ENVR.KW.PEV.HHCP..PILLVGTK.DLR...DT..RL.....APIT..
Retrocopy SYPQTNVFVICFSIASPPSYENVRHKWHPEVCHHCPDVPILLVGTKKDLRAQPDTLRRLKEQGQAPITPQ

Parental  QGLAMAREIGSVKYLECSALTQRGLKTVFDEAIRAVLCPPPVKKPGKKCTV
          QG.A.A..I..V.YLECSAL.Q.G.K.VF.EA.RAVL.P.P.K..G..C..
Retrocopy QGQALAKQIHAVRYLECSALQQDGVKEVFAEAVRAVLNPTPIKR-GRSCVL

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	18.87 RPM	22.09 RPM
SRP017611_kidney	10.57 RPM	4.92 RPM
SRP017611_liver	21.59 RPM	2.31 RPM
SRP040447_lung	70.82 RPM	34.63 RPM
SRP040447_skeletal_muscle	15.46 RPM	1.95 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_18 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_18 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 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017364	1 retrocopy	retro_amel_1104,
Callithrix jacchus	ENSCJAG00000018194	1 retrocopy	retro_cjac_2687,
Cavia porcellus	ENSCPOG00000006543	4 retrocopies	retro_cpor_1168, retro_cpor_286, retro_cpor_33, retro_cpor_887,
Cavia porcellus	ENSCPOG00000013861	1 retrocopy	retro_cpor_18 ,
Echinops telfairi	ENSETEG00000012902	3 retrocopies	retro_etel_1565, retro_etel_1645, retro_etel_42,
Macropus eugenii	ENSMEUG00000006196	1 retrocopy	retro_meug_201,
Otolemur garnettii	ENSOGAG00000012467	1 retrocopy	retro_ogar_2140,
Procavia capensis	ENSPCAG00000009949	1 retrocopy	retro_pcap_16,
Pongo abelii	ENSPPYG00000008763	2 retrocopies	retro_pabe_1047, retro_pabe_2546,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Takifugu rubripes	ENSTRUG00000016201	1 retrocopy	retro_trub_15,