RetrogeneDB ID: retro_cpor_178

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:48402480..48402683(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS18C
• Ensembl ID: ENSCPOG00000009198
• Aliases: None
• Description: None

Sequence

>retro_cpor_178
TCCTTAGAAGGACCCTTTAAAAAAAAAAGTGCATCTTGTGTGGCAAATGTGGAGTATAAGCCCGTGCAGCTTTTGTCCCA
GTTTATGTCTTCATATACTGGATGCGTTCATGGGAGGCATATAACAGGTCTGTAGGAAGAAACAAAAGTTTCAAAGGCAA
TTAAGAGAGCTAGATAATGGGGTTAATGCCAGTAATATACAAG

Alignment

ORF - retro_cpor_178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.7 %
• Parental protein coverage: 50.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TMENPYKEPLKKCILCGKRVDYKNVQLLSQFISAYTGCIHGRHITGLCGKKQKEISKAIKRAQ-VMGFMP
          ..E.P.......C......V.YK.VQLLSQF.S.YTGC.HGRHITGL........SKAIKRA...MG.MP
Retrocopy SLEGPFXXXXASCVA---NVEYKPVQLLSQFMSSYTGCVHGRHITGL--*EETKVSKAIKRAR<IMGLMP

Parental  VTHK
          V..K
Retrocopy VIYK

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	0.40 RPM	17.08 RPM
SRP017611_kidney	0.21 RPM	12.25 RPM
SRP017611_liver	0.22 RPM	16.10 RPM
SRP040447_lung	0.23 RPM	9.99 RPM
SRP040447_skeletal_muscle	0.31 RPM	12.60 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_178 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_178 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.

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018155	3 retrocopies	retro_btau_1386, retro_btau_309, retro_btau_502,
Callithrix jacchus	ENSCJAG00000005286	3 retrocopies	retro_cjac_1419, retro_cjac_234, retro_cjac_3970,
Cavia porcellus	ENSCPOG00000009198	1 retrocopy	retro_cpor_178 ,
Dasypus novemcinctus	ENSDNOG00000018326	2 retrocopies	retro_dnov_1030, retro_dnov_152,
Homo sapiens	ENSG00000163319	5 retrocopies	retro_hsap_1540, retro_hsap_2597, retro_hsap_4019, retro_hsap_4684, retro_hsap_969,
Gorilla gorilla	ENSGGOG00000008603	2 retrocopies	retro_ggor_1173, retro_ggor_2908,
Macropus eugenii	ENSMEUG00000010972	2 retrocopies	retro_meug_104, retro_meug_1113,
Myotis lucifugus	ENSMLUG00000017057	1 retrocopy	retro_mluc_2360,
Macaca mulatta	ENSMMUG00000015353	4 retrocopies	retro_mmul_2203, retro_mmul_2494, retro_mmul_655, retro_mmul_793,
Mus musculus	ENSMUSG00000016833	2 retrocopies	retro_mmus_1546, retro_mmus_2127,
Nomascus leucogenys	ENSNLEG00000009119	4 retrocopies	retro_nleu_111, retro_nleu_1614, retro_nleu_2722, retro_nleu_3010,
Ochotona princeps	ENSOPRG00000004113	2 retrocopies	retro_opri_1041, retro_opri_966,
Pongo abelii	ENSPPYG00000025867	2 retrocopies	retro_pabe_1276, retro_pabe_70,
Pan troglodytes	ENSPTRG00000016233	3 retrocopies	retro_ptro_1039, retro_ptro_1521, retro_ptro_3113,
Pteropus vampyrus	ENSPVAG00000006439	2 retrocopies	retro_pvam_1326, retro_pvam_1412,
Rattus norvegicus	ENSRNOG00000002178	3 retrocopies	retro_rnor_2264, retro_rnor_2265, retro_rnor_477,
Sarcophilus harrisii	ENSSHAG00000007084	1 retrocopy	retro_shar_718,
Ictidomys tridecemlineatus	ENSSTOG00000007989	1 retrocopy	retro_itri_1231,
Tupaia belangeri	ENSTBEG00000012505	3 retrocopies	retro_tbel_1755, retro_tbel_4724, retro_tbel_508,
Tarsius syrichta	ENSTSYG00000012924	1 retrocopy	retro_tsyr_649,
Tursiops truncatus	ENSTTRG00000004897	2 retrocopies	retro_ttru_144, retro_ttru_1721,