RetrogeneDB ID: retro_cpor_305

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_12:29792759..29793099(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000004321
• Aliases: None
• Description: None

Sequence

>retro_cpor_305
ATGGCCTCTATCTCTGAGCTCACCTGCATCCACTCTGACCTTATCCTGCAGGACTGTGAAGTGACCGTCATGAAGGACAA
GATCAATGCCCTTATTAAAGTGGCTGGTGTCAATGTCCAGCCTTTTTGGACTGGCTTGTGTGCAAAGGCCCTGGTCAGTG
TCAAATTGATGTGTTCATCTGCAGTGTAGGGACTAGTGACCCTGCTCCCTCAGCTGGTGCTGCCCCTAGAGGAGGCCCTC
CCCTCCCCACCACTGCTGCCTCGGTGAGGAGAAGAAGGTAGAAGCCAAGAGAGAAGAATCTGAGGAGTCTGATGATGACA
TGGGCTTTGGTCTTTTTGAC

Alignment

ORF - retro_cpor_305 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASVSELACIYSALILHDDEVTVTEDKINALIKAAGVNVEPFWPGLFAKALANV-SIGSLICNVGAGGPA
          MAS.SEL.CI.S.LIL.D.EVTV..DKINALIK.AGVNV.PFW.GL.AKAL..V..I...IC.VG...PA
Retrocopy MASISELTCIHSDLILQDCEVTVMKDKINALIKVAGVNVQPFWTGLCAKALVSV<QIDVFICSVGTSDPA

Parental  PAAGAAPAGSPAPTTTAAP-AEEKKVEAKKEESEESDDDMGFGLFD
          P.AGAAP.G.P...TTAA...EEKKVEAK.EESEESDDDMGFGLFD
Retrocopy PSAGAAPRGGPPLPTTAAS<GEEKKVEAKREESEESDDDMGFGLFD

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	136.14 RPM
SRP017611_kidney	0.00 RPM	264.86 RPM
SRP017611_liver	0.00 RPM	118.09 RPM
SRP040447_lung	0.00 RPM	344.84 RPM
SRP040447_skeletal_muscle	0.00 RPM	858.33 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_305 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_305 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 12 parental genes, and 107 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014251	20 retrocopies	retro_amel_1030, retro_amel_1076, retro_amel_110, retro_amel_1152, retro_amel_1191, retro_amel_128, retro_amel_1343, retro_amel_1345, retro_amel_1354, retro_amel_1428, retro_amel_161, retro_amel_1694, retro_amel_1696, retro_amel_1705, retro_amel_1852, retro_amel_205, retro_amel_316, retro_amel_395, retro_amel_404, retro_amel_769,
Cavia porcellus	ENSCPOG00000004321	6 retrocopies	retro_cpor_1011, retro_cpor_1058, retro_cpor_260, retro_cpor_305 , retro_cpor_667, retro_cpor_75,
Dasypus novemcinctus	ENSDNOG00000014224	26 retrocopies	retro_dnov_1130, retro_dnov_1325, retro_dnov_1410, retro_dnov_1439, retro_dnov_146, retro_dnov_1467, retro_dnov_1580, retro_dnov_1660, retro_dnov_1667, retro_dnov_17, retro_dnov_1748, retro_dnov_179, retro_dnov_1878, retro_dnov_1911, retro_dnov_1967, retro_dnov_20, retro_dnov_2075, retro_dnov_2234, retro_dnov_240, retro_dnov_2421, retro_dnov_2618, retro_dnov_2640, retro_dnov_405, retro_dnov_561, retro_dnov_601, retro_dnov_746,
Latimeria chalumnae	ENSLACG00000012630	1 retrocopy	retro_lcha_7,
Macropus eugenii	ENSMEUG00000015277	6 retrocopies	retro_meug_1096, retro_meug_1283, retro_meug_1312, retro_meug_1401, retro_meug_1515, retro_meug_793,
Macropus eugenii	ENSMEUG00000015282	2 retrocopies	retro_meug_207, retro_meug_45,
Monodelphis domestica	ENSMODG00000009209	1 retrocopy	retro_mdom_1022,
Monodelphis domestica	ENSMODG00000009218	4 retrocopies	retro_mdom_1168, retro_mdom_2001, retro_mdom_385, retro_mdom_50,
Oryctolagus cuniculus	ENSOCUG00000015087	8 retrocopies	retro_ocun_1009, retro_ocun_1464, retro_ocun_1655, retro_ocun_1735, retro_ocun_48, retro_ocun_551, retro_ocun_647, retro_ocun_884,
Ochotona princeps	ENSOPRG00000001163	11 retrocopies	retro_opri_1010, retro_opri_130, retro_opri_214, retro_opri_245, retro_opri_38, retro_opri_530, retro_opri_645, retro_opri_768, retro_opri_784, retro_opri_96, retro_opri_972,
Sarcophilus harrisii	ENSSHAG00000014818	6 retrocopies	retro_shar_182, retro_shar_234, retro_shar_449, retro_shar_550, retro_shar_614, retro_shar_742,
Sus scrofa	ENSSSCG00000004970	16 retrocopies	retro_sscr_1105, retro_sscr_1165, retro_sscr_1184, retro_sscr_1185, retro_sscr_16, retro_sscr_176, retro_sscr_18, retro_sscr_259, retro_sscr_307, retro_sscr_323, retro_sscr_4, retro_sscr_47, retro_sscr_583, retro_sscr_776, retro_sscr_904, retro_sscr_923,