RetrogeneDB ID: retro_cpor_193

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:45606751..45607333(-)
• Located in intron of: ENSCPOG00000000630

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCBP2
• Ensembl ID: ENSCPOG00000000967
• Aliases: None
• Description: None

Sequence

>retro_cpor_193
ATACTCAACATGGACAACAGTGAGACTGAAGGAGGATTAAATGCCACTCTCACCATCTGGTTACTTATGCATGGAAAGGA
AGTTGGCAGTATCTTTGGAAAGAAAGGAGAGTCAGATAAGAAAATGTGCAAAGAGAGTGGTGAGGGTATCAGCATCTCAG
GAGGGAACTGTACTGAGTGAATTATTGCTCTGGCTGGACTTACTAAAGCCATCTTCAAAACCTTTGCTATGATCATTGAC
AAACTGGAAGAGGACATCAGCAACTCTATGACCAAAAGCACAGTGCCAGTAGACCCCTGGCCACTCTGAGGCTGGTGGTC
CCTGCTAGTAAATGCAGCTGTCTCATTGGAAAAGGTGGTTGCAAGATCAAGGAAATATGAGAGAGGACCAGGGGCTCTGG
TCCAAGTGGAGGGAGACATGCTCCCCAACTCAACTGAGCGGGCCATCACTATTGCTGGCATCCTGCAATCCATCATTGAG
CTTGTCAGACAGATCTGAGTGGTCATGTTGGAGGCTGCCCTGAAGGGCGTGATTATCCCTTACTGGCCCAAGCCATCAAA
TTCTCCAGTCATTTTTCCTGGT

Alignment

ORF - retro_cpor_193 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.53 %
• Parental protein coverage: 52.01 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ILDMDTGVIEGGLNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNA
          IL.MD....EGGLN.TLTI.LLMHGKEVGSI.GKKGES.KKM..ESG..I.IS.GNC.E.II.LAG.T.A
Retrocopy ILNMDNSETEGGLNATLTIWLLMHGKEVGSIFGKKGESDKKMCKESGEGISISGGNCTE*IIALAGLTKA

Parental  IFKAFAMIIDKLEEDISSSMTNST-AASRPPVTLRLVVPASQCGSLIGKGGCKIKEIREST-GAQVQVAG
          IFK.FAMIIDKLEEDIS.SMT.ST..ASRP..TLRLVVPAS.C..LIGKGGCKIKEI.E.T.GA.VQV.G
Retrocopy IFKTFAMIIDKLEEDISNSMTKST<SASRPLATLRLVVPASKCSCLIGKGGCKIKEI*ERT>GALVQVEG

Parental  DMLPNSTERAITIAGIPQSIIECVKQICVVMLESPPKGVTIPYRPKPSSSPVIFAG
          DMLPNSTERAITIAGI.QSIIE.V.QI.VVMLE...KGV.IPY.PKPS.SPVIF.G
Retrocopy DMLPNSTERAITIAGILQSIIELVRQI*VVMLEAALKGVIIPYWPKPSNSPVIFPG

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	201.71 RPM
SRP017611_kidney	0.00 RPM	395.30 RPM
SRP017611_liver	0.00 RPM	274.26 RPM
SRP040447_lung	0.00 RPM	293.75 RPM
SRP040447_skeletal_muscle	0.01 RPM	234.53 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_193 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_193 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 26 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020757	1 retrocopy	retro_btau_175,
Canis familiaris	ENSCAFG00000006821	1 retrocopy	retro_cfam_54,
Callithrix jacchus	ENSCJAG00000018590	2 retrocopies	retro_cjac_3253, retro_cjac_754,
Cavia porcellus	ENSCPOG00000000967	2 retrocopies	retro_cpor_193 , retro_cpor_97,
Cavia porcellus	ENSCPOG00000003648	1 retrocopy	retro_cpor_257,
Dasypus novemcinctus	ENSDNOG00000008688	6 retrocopies	retro_dnov_1146, retro_dnov_1399, retro_dnov_1672, retro_dnov_1823, retro_dnov_2434, retro_dnov_452,
Equus caballus	ENSECAG00000022389	1 retrocopy	retro_ecab_67,
Erinaceus europaeus	ENSEEUG00000001077	2 retrocopies	retro_eeur_218, retro_eeur_655,
Echinops telfairi	ENSETEG00000014741	3 retrocopies	retro_etel_1170, retro_etel_2108, retro_etel_840,
Homo sapiens	ENSG00000197111	2 retrocopies	retro_hsap_4077, retro_hsap_83,
Gorilla gorilla	ENSGGOG00000012613	2 retrocopies	retro_ggor_212, retro_ggor_2734,
Macropus eugenii	ENSMEUG00000001887	7 retrocopies	retro_meug_1143, retro_meug_1988, retro_meug_432, retro_meug_526, retro_meug_618, retro_meug_828, retro_meug_964,
Microcebus murinus	ENSMICG00000011651	2 retrocopies	retro_mmur_1226, retro_mmur_1228,
Myotis lucifugus	ENSMLUG00000009971	3 retrocopies	retro_mluc_2199, retro_mluc_314, retro_mluc_571,
Macaca mulatta	ENSMMUG00000006608	2 retrocopies	retro_mmul_1263, retro_mmul_1994,
Mus musculus	ENSMUSG00000056851	1 retrocopy	retro_mmus_274,
Nomascus leucogenys	ENSNLEG00000017693	1 retrocopy	retro_nleu_10,
Oryctolagus cuniculus	ENSOCUG00000022490	3 retrocopies	retro_ocun_10, retro_ocun_1622, retro_ocun_898,
Ochotona princeps	ENSOPRG00000004680	5 retrocopies	retro_opri_1126, retro_opri_284, retro_opri_313, retro_opri_742, retro_opri_789,
Pongo abelii	ENSPPYG00000004581	2 retrocopies	retro_pabe_3346, retro_pabe_92,
Pan troglodytes	ENSPTRG00000005018	1 retrocopy	retro_ptro_113,
Pteropus vampyrus	ENSPVAG00000012284	3 retrocopies	retro_pvam_1168, retro_pvam_1369, retro_pvam_868,
Rattus norvegicus	ENSRNOG00000036852	2 retrocopies	retro_rnor_1238, retro_rnor_2088,
Sus scrofa	ENSSSCG00000000274	1 retrocopy	retro_sscr_61,
Ictidomys tridecemlineatus	ENSSTOG00000003635	2 retrocopies	retro_itri_1522, retro_itri_557,
Vicugna pacos	ENSVPAG00000000406	1 retrocopy	retro_vpac_471,