RetrogeneDB ID: retro_cpor_1086

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_45:15399238..15399509(+)
• Located in intron of: ENSCPOG00000013530

Retrocopy information

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

Parental gene information

• Parental gene symbol: UQCRB
• Ensembl ID: ENSCPOG00000012149
• Aliases: None
• Description: None

Sequence

>retro_cpor_1086
TGGCCGGACACTGTTCGGAAGTGGTGTGACAGTGCTGCGGACTCAGCAAGCTGGGCTAACTGTGAGAGGATGCAGTAGAA
GATGATGATGTAAAAGAAGCCATAAAAGGCTTCCCAAGGACCTGTATAGCGGCAGGCTGTTTCGAAGTAAGAGCGCACTG
GACCTGAGCCTGAAGCATCAGATCCTGCCTGGAGAGCGCTGGACAGACCAGGAGGAGGGTAAATAATATCTGAACCACAT
CTCACAGGTTATTTGGGGCAGAAAAGAGAGA

Alignment

ORF - retro_cpor_1086 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.84 %
• Parental protein coverage: 83.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WLDSFRKWYYNAA-GFNKLGLMRDDTIYEDEDVKEAIR-RLPENLYNDRMFRIKRALDLSMKHQILPKEQ
          W.D..RKW...AA.G..KLG....D...ED.DVKEAI..RLP..LY..R.FR.K.ALDLS.KHQILP.E.
Retrocopy WPDTVRKWCDSAA<GLSKLG*L*EDAV-EDDDVKEAIK<RLPKDLYSGRLFRSKSALDLSLKHQILPGER

Parental  WTKYEEDKFYLEPYLKEVIRERKER
          WT..EE.K.YL......VI..RKER
Retrocopy WTDQEEGK*YLN-HISQVIWGRKER

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	0.12 RPM	31.75 RPM
SRP017611_kidney	0.00 RPM	88.67 RPM
SRP017611_liver	0.00 RPM	55.63 RPM
SRP040447_lung	0.05 RPM	20.61 RPM
SRP040447_skeletal_muscle	0.00 RPM	144.31 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1086 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1086 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 23 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007287	1 retrocopy	retro_amel_985,
Canis familiaris	ENSCAFG00000009449	4 retrocopies	retro_cfam_1504, retro_cfam_1509, retro_cfam_1531, retro_cfam_792,
Callithrix jacchus	ENSCJAG00000020560	2 retrocopies	retro_cjac_2206, retro_cjac_894,
Cavia porcellus	ENSCPOG00000012149	2 retrocopies	retro_cpor_1086 , retro_cpor_866,
Erinaceus europaeus	ENSEEUG00000001312	1 retrocopy	retro_eeur_224,
Felis catus	ENSFCAG00000026302	5 retrocopies	retro_fcat_1292, retro_fcat_178, retro_fcat_1780, retro_fcat_378, retro_fcat_558,
Homo sapiens	ENSG00000156467	2 retrocopies	retro_hsap_3261, retro_hsap_4838,
Gorilla gorilla	ENSGGOG00000026528	1 retrocopy	retro_ggor_3017,
Latimeria chalumnae	ENSLACG00000004465	1 retrocopy	retro_lcha_127,
Loxodonta africana	ENSLAFG00000002542	1 retrocopy	retro_lafr_727,
Myotis lucifugus	ENSMLUG00000007182	1 retrocopy	retro_mluc_1601,
Macaca mulatta	ENSMMUG00000008804	3 retrocopies	retro_mmul_2053, retro_mmul_2065, retro_mmul_2581,
Mus musculus	ENSMUSG00000021520	4 retrocopies	retro_mmus_1175, retro_mmus_1628, retro_mmus_2610, retro_mmus_514,
Nomascus leucogenys	ENSNLEG00000026670	1 retrocopy	retro_nleu_1357,
Oryctolagus cuniculus	ENSOCUG00000008113	3 retrocopies	retro_ocun_1149, retro_ocun_345, retro_ocun_570,
Otolemur garnettii	ENSOGAG00000004302	1 retrocopy	retro_ogar_1451,
Ochotona princeps	ENSOPRG00000008892	2 retrocopies	retro_opri_109, retro_opri_688,
Pongo abelii	ENSPPYG00000018763	2 retrocopies	retro_pabe_2703, retro_pabe_3762,
Rattus norvegicus	ENSRNOG00000024967	1 retrocopy	retro_rnor_290,
Sorex araneus	ENSSARG00000002999	3 retrocopies	retro_sara_460, retro_sara_52, retro_sara_704,
Ictidomys tridecemlineatus	ENSSTOG00000008017	1 retrocopy	retro_itri_46,
Tarsius syrichta	ENSTSYG00000010502	2 retrocopies	retro_tsyr_1114, retro_tsyr_898,
Drosophila melanogaster	FBgn0030733	1 retrocopy	retro_dmel_22,