RetrogeneDB ID: retro_cpor_479

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_165:1072994..1073327(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5G3
• Ensembl ID: ENSCPOG00000006194
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C3 (subunit 9) [Source:HGNC Symbol;Acc:843]

Sequence

>retro_cpor_479
TTTGCCCACACCAACCTCACCTGTACCCTGCTCTGATCCAAGCTGGAGCCAGAGTAGCATACAGATCATTTCTGCATCAG
TTTTACCTCAGCTGGAGGCTAGGACTAGAGAGAGCTCTACAGCATTTAATGGGGCCCAGAGCAGGGTGTGTCAGCTAATC
AGAAGGGAGTTTCAGACCAGTGCAATTAGCAGAGACATTGATACTGCTGCCCAGTTTATTGGTCCAGGTGCTACAGCAAT
AGAAGTGGCTGGTCTGGGCGCTGGTATCAAAGTCTCTGGCAGCCTTGCCATTGCTTACGCCTTACACCTTTGTTGAAACA
GTAGCTGTTCTCA

Alignment

ORF - retro_cpor_479 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.97 %
• Parental protein coverage: 80.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FACAKLACT-PALIRAGSRVAYRP-ISASVLSRPETRTGEGSLVFNGAQNGVCQLIRREFQTSAISRDID
          FA...L.CT.PALI.AG.RVAYR..ISASVL...E.RT.E.S..FNGAQ..VCQLIRREFQTSAISRDID
Retrocopy FAHTNLTCT<PALIQAGARVAYRS<ISASVLPQLEARTRESSTAFNGAQSRVCQLIRREFQTSAISRDID

Parental  TAAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARN-PSLKQQLFS
          TAA.FIG.GA....VAG.GAGI..V.GSL.I.YA...P.LKQ.LFS
Retrocopy TAAQFIGPGATAIEVAGLGAGI-KVSGSLAIAYALH<PLLKQ*LFS

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	99.96 RPM
SRP017611_kidney	0.00 RPM	274.39 RPM
SRP017611_liver	0.00 RPM	154.61 RPM
SRP040447_lung	0.00 RPM	74.12 RPM
SRP040447_skeletal_muscle	0.00 RPM	369.53 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_479 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_479 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 19 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012367	1 retrocopy	retro_amel_1829,
Canis familiaris	ENSCAFG00000013366	2 retrocopies	retro_cfam_4, retro_cfam_5,
Choloepus hoffmanni	ENSCHOG00000012592	3 retrocopies	retro_chof_189, retro_chof_2561, retro_chof_508,
Callithrix jacchus	ENSCJAG00000008207	3 retrocopies	retro_cjac_279, retro_cjac_38, retro_cjac_4183,
Cavia porcellus	ENSCPOG00000006194	1 retrocopy	retro_cpor_479 ,
Cavia porcellus	ENSCPOG00000009017	2 retrocopies	retro_cpor_43, retro_cpor_550,
Cavia porcellus	ENSCPOG00000022889	3 retrocopies	retro_cpor_1495, retro_cpor_268, retro_cpor_492,
Dasypus novemcinctus	ENSDNOG00000010440	2 retrocopies	retro_dnov_235, retro_dnov_396,
Loxodonta africana	ENSLAFG00000010768	1 retrocopy	retro_lafr_120,
Myotis lucifugus	ENSMLUG00000012822	1 retrocopy	retro_mluc_23,
Macaca mulatta	ENSMMUG00000003954	1 retrocopy	retro_mmul_148,
Monodelphis domestica	ENSMODG00000009520	3 retrocopies	retro_mdom_1070, retro_mdom_295, retro_mdom_545,
Mustela putorius furo	ENSMPUG00000013986	1 retrocopy	retro_mputfur_818,
Oryctolagus cuniculus	ENSOCUG00000012164	1 retrocopy	retro_ocun_949,
Otolemur garnettii	ENSOGAG00000027578	1 retrocopy	retro_ogar_1938,
Rattus norvegicus	ENSRNOG00000001596	1 retrocopy	retro_rnor_1106,
Sorex araneus	ENSSARG00000006733	1 retrocopy	retro_sara_82,
Ictidomys tridecemlineatus	ENSSTOG00000013572	4 retrocopies	retro_itri_1091, retro_itri_1236, retro_itri_324, retro_itri_438,
Tupaia belangeri	ENSTBEG00000012159	1 retrocopy	retro_tbel_54,