RetrogeneDB ID: retro_cpor_1018

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:37474017..37474333(+)
• Located in intron of: ENSCPOG00000008670

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS19
• Ensembl ID: ENSCPOG00000025140
• Aliases: None
• Description: None

Sequence

>retro_cpor_1018
TCCCTTTTCCCTGGCTGGCAGCACCGAGGCCAAGAGCTGCCCAGAGTTATAGTAAAAGACGTACACAGCAGGAATTTGTC
GGAGCTCTGGCCTCCTTCCTCAGAAAGTCTGGGAAGCTGAAAGTCCCCGAATGGGTAGATACAGGCAAGCTGGCCGAGCA
TAAAGAGCATGCTTCCTACAATGACGACCGTTTCTACACATGAGCTGCTTCTACAGCACAGCACCTGTACCTCTGAGGTG
GTCCTGGGCAGGCTCCATGACCAAGATCTATGGTGGACATCAAAGGAGTAGCGTCATGTCAGCTGAGGCTCCAAGA

Alignment

ORF - retro_cpor_1018 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.59 %
• Parental protein coverage: 67.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLSPGWQRGGRTMPGVTVKDVN-QQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRA
          SL.PGWQ..G...P.V.VKDV..QQEFV.ALA.FL.KSGKLKVPEWVDT.KLA.HKE.A.Y....FYT.A
Retrocopy SLFPGWQHRGQELPRVIVKDVH<QQEFVGALASFLRKSGKLKVPEWVDTGKLAEHKEHASYNDDRFYT*A

Parental  ASTARHLYLRGGAG-VGSMTKIYGGRQRNGVMPSHFSR
          ASTA.HLYL.GG.G..GSMTKIYGG.QR..VM.....R
Retrocopy ASTAQHLYL*GGPG<AGSMTKIYGGHQRSSVMSAEAPR

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	96.51 RPM
SRP017611_kidney	0.00 RPM	184.15 RPM
SRP017611_liver	0.00 RPM	169.28 RPM
SRP040447_lung	0.00 RPM	229.08 RPM
SRP040447_skeletal_muscle	0.00 RPM	212.88 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1018 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1018 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 15 parental genes, and 82 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004456	4 retrocopies	retro_amel_1418, retro_amel_1816, retro_amel_193, retro_amel_550,
Canis familiaris	ENSCAFG00000028485	10 retrocopies	retro_cfam_1017, retro_cfam_1074, retro_cfam_1155, retro_cfam_1251, retro_cfam_1377, retro_cfam_149, retro_cfam_1998, retro_cfam_2212, retro_cfam_249, retro_cfam_499,
Callithrix jacchus	ENSCJAG00000020243	5 retrocopies	retro_cjac_1968, retro_cjac_2004, retro_cjac_2094, retro_cjac_2324, retro_cjac_3,
Cavia porcellus	ENSCPOG00000025140	1 retrocopy	retro_cpor_1018 ,
Felis catus	ENSFCAG00000008125	3 retrocopies	retro_fcat_2026, retro_fcat_543, retro_fcat_816,
Gorilla gorilla	ENSGGOG00000015279	4 retrocopies	retro_ggor_1085, retro_ggor_1503, retro_ggor_2458, retro_ggor_578,
Myotis lucifugus	ENSMLUG00000006143	5 retrocopies	retro_mluc_1316, retro_mluc_2247, retro_mluc_2426, retro_mluc_980, retro_mluc_987,
Pongo abelii	ENSPPYG00000010029	7 retrocopies	retro_pabe_1158, retro_pabe_1754, retro_pabe_1781, retro_pabe_2636, retro_pabe_430, retro_pabe_585, retro_pabe_586,
Pan troglodytes	ENSPTRG00000011037	6 retrocopies	retro_ptro_1392, retro_ptro_2269, retro_ptro_2467, retro_ptro_485, retro_ptro_612, retro_ptro_961,
Pteropus vampyrus	ENSPVAG00000008980	4 retrocopies	retro_pvam_1032, retro_pvam_1171, retro_pvam_137, retro_pvam_895,
Rattus norvegicus	ENSRNOG00000048199	3 retrocopies	retro_rnor_221, retro_rnor_299, retro_rnor_51,
Sarcophilus harrisii	ENSSHAG00000006831	1 retrocopy	retro_shar_731,
Sus scrofa	ENSSSCG00000003042	3 retrocopies	retro_sscr_1064, retro_sscr_308, retro_sscr_58,
Tupaia belangeri	ENSTBEG00000003457	21 retrocopies	retro_tbel_103, retro_tbel_1275, retro_tbel_1575, retro_tbel_1748, retro_tbel_1803, retro_tbel_1888, retro_tbel_2104, retro_tbel_2521, retro_tbel_2554, retro_tbel_2971, retro_tbel_3008, retro_tbel_3339, retro_tbel_3388, retro_tbel_345, retro_tbel_3607, retro_tbel_3860, retro_tbel_4425, retro_tbel_673, retro_tbel_875, retro_tbel_913, retro_tbel_945,
Tursiops truncatus	ENSTTRG00000008278	5 retrocopies	retro_ttru_1308, retro_ttru_1608, retro_ttru_1686, retro_ttru_336, retro_ttru_593,