RetrogeneDB ID: retro_cpor_860

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:49793377..49793716(-)
• Located in intron of: ENSCPOG00000001976

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS18
• Ensembl ID: ENSCPOG00000019675
• Aliases: None
• Description: None

Sequence

>retro_cpor_860
CTAGTGATCACTGAGACGCTCCACCACATTCTGCTGGTACTCAACATCAACACTGGTGAGTGATGGTAGACAGTCTTTTC
CATCACTGCCATTAAGGATGTGTGGGCAAAGATATGCTCCTGTGATGCTGAGGAAAGCAGAAGGGGACCTCACCAGAAGG
GCTGGAGAACTCCCTGAGGCTGAGGTGGAGCACATGATCACTAGCATGCAGAATCCCTGCCAGTGCACAATCACAGACCA
GTTCCGAATCAGACAGCAGGTGGAGAAGATGTGAAATATAGCAGGGCTCTAGCCAGTGGTCTGGATATCAAGCTCCATGA
AGATCTGGAGTGACTGAGG

Alignment

ORF - retro_cpor_860 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.13 %
• Parental protein coverage: 74.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGV-GRRYAHVVLRKADIDLTKRAGELTEDEVERVITIM
          LVI.E...HIL.VLN.N........F.ITAIK.V.G.RYA.V.LRKA..DLT.RAGEL.E.EVE..IT.M
Retrocopy LVITETLHHILLVLNINTGE*W*TVFSITAIKDV>GQRYAPVMLRKAEGDLTRRAGELPEAEVEHMITSM

Parental  QNPRQYKIPDWFLNRQKDVK-DGKYSQVLANGLDNKLREDLERLK
          QNP.Q..I.D.F..RQ...K.D.KYS..LA.GLD.KL.EDLE.L.
Retrocopy QNPCQCTITDQFRIRQQVEK<DVKYSRALASGLDIKLHEDLE*LR

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	122.17 RPM
SRP017611_kidney	0.00 RPM	218.69 RPM
SRP017611_liver	0.00 RPM	128.32 RPM
SRP040447_lung	0.00 RPM	288.00 RPM
SRP040447_skeletal_muscle	0.00 RPM	328.03 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_860 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_860 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 16 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002918	1 retrocopy	retro_acar_206,
Ailuropoda melanoleuca	ENSAMEG00000001623	2 retrocopies	retro_amel_1617, retro_amel_381,
Cavia porcellus	ENSCPOG00000019675	4 retrocopies	retro_cpor_1044, retro_cpor_130, retro_cpor_860 , retro_cpor_971,
Felis catus	ENSFCAG00000004013	7 retrocopies	retro_fcat_1058, retro_fcat_1536, retro_fcat_166, retro_fcat_222, retro_fcat_313, retro_fcat_327, retro_fcat_430,
Gorilla gorilla	ENSGGOG00000006571	5 retrocopies	retro_ggor_1496, retro_ggor_2310, retro_ggor_344, retro_ggor_77, retro_ggor_93,
Loxodonta africana	ENSLAFG00000032173	1 retrocopy	retro_lafr_1171,
Myotis lucifugus	ENSMLUG00000007360	2 retrocopies	retro_mluc_181, retro_mluc_932,
Macaca mulatta	ENSMMUG00000003867	1 retrocopy	retro_mmul_2198,
Mustela putorius furo	ENSMPUG00000002306	6 retrocopies	retro_mputfur_1110, retro_mputfur_1204, retro_mputfur_399, retro_mputfur_687, retro_mputfur_888, retro_mputfur_943,
Oryctolagus cuniculus	ENSOCUG00000010546	1 retrocopy	retro_ocun_31,
Pongo abelii	ENSPPYG00000025953	14 retrocopies	retro_pabe_1138, retro_pabe_128, retro_pabe_1481, retro_pabe_1482, retro_pabe_1813, retro_pabe_1881, retro_pabe_2303, retro_pabe_2407, retro_pabe_2663, retro_pabe_2833, retro_pabe_2967, retro_pabe_3013, retro_pabe_3070, retro_pabe_368,
Pan troglodytes	ENSPTRG00000018039	1 retrocopy	retro_ptro_121,
Rattus norvegicus	ENSRNOG00000028505	4 retrocopies	retro_rnor_102, retro_rnor_234, retro_rnor_29, retro_rnor_70,
Sarcophilus harrisii	ENSSHAG00000006857	2 retrocopies	retro_shar_265, retro_shar_563,
Sarcophilus harrisii	ENSSHAG00000008658	1 retrocopy	retro_shar_618,
Ictidomys tridecemlineatus	ENSSTOG00000002417	13 retrocopies	retro_itri_1023, retro_itri_1049, retro_itri_1121, retro_itri_1316, retro_itri_1484, retro_itri_228, retro_itri_397, retro_itri_547, retro_itri_690, retro_itri_742, retro_itri_854, retro_itri_875, retro_itri_878,