RetrogeneDB ID: retro_cpor_335

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_13:16554304..16554613(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS8
• Ensembl ID: ENSCPOG00000000723
• Aliases: None
• Description: 40S ribosomal protein S8 [Source:UniProtKB/TrEMBL;Acc:H0UUK1]

Sequence

>retro_cpor_335
GGCATCTCTCAGGACAACTGGCACAAGACCAGGAGCAAAAGAAAGCCCAAGAAGTGGAAGTATGAGTTGGGTTGCCCAGC
TGCCAGCACTAAGATTGGCCCCCACCAAATACACACAGTTGAGTTCAAGGAGGCAACAAGAGGCAGTGAGCCCTCAGGCT
GGATACTGGAAACTTCTCCTGGGACTCTTGAGTGTTATACTTGAAAAACAAGGATCACTGACATTGTTTACAATGTGTCC
AATAATGAGCTGGTATGCACCAAGACCCTGGTGAAGAACGGCACTGTGCTCATTGATAGCGTGCTCTAC

Alignment

ORF - retro_cpor_335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.91 %
• Parental protein coverage: 57.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVR-VRGGNKKYRALRLDVGNFSWGS-
          GIS.DNWH...KT..KRKP..KK.KYELG.PAA.TKIGP..IHTV..V.GGNK...ALRLD.GNFSW.S.
Retrocopy GISQDNWH---KTRSKRKP--KKWKYELGCPAASTKIGPHQIHTVE<VQGGNKRQ*ALRLDTGNFSWDS>

Parental  ECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPY
          EC.T.KTRI.D.VYN.SNNELV.TKTLVKN..VLIDS..Y
Retrocopy ECYT*KTRITDIVYNVSNNELVCTKTLVKNGTVLIDSVLY

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	204.18 RPM
SRP017611_kidney	0.00 RPM	317.10 RPM
SRP017611_liver	0.00 RPM	171.58 RPM
SRP040447_lung	0.00 RPM	379.62 RPM
SRP040447_skeletal_muscle	0.00 RPM	475.05 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_335 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_335 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 92 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015285	2 retrocopies	retro_btau_1388, retro_btau_1593,
Canis familiaris	ENSCAFG00000004745	8 retrocopies	retro_cfam_1336, retro_cfam_1662, retro_cfam_1730, retro_cfam_2139, retro_cfam_2177, retro_cfam_261, retro_cfam_589, retro_cfam_791,
Callithrix jacchus	ENSCJAG00000004197	5 retrocopies	retro_cjac_1068, retro_cjac_181, retro_cjac_3138, retro_cjac_6, retro_cjac_951,
Cavia porcellus	ENSCPOG00000000723	3 retrocopies	retro_cpor_1099, retro_cpor_335 , retro_cpor_621,
Dipodomys ordii	ENSDORG00000009287	1 retrocopy	retro_dord_429,
Felis catus	ENSFCAG00000022996	4 retrocopies	retro_fcat_1222, retro_fcat_200, retro_fcat_456, retro_fcat_962,
Gorilla gorilla	ENSGGOG00000005645	5 retrocopies	retro_ggor_1127, retro_ggor_1170, retro_ggor_1357, retro_ggor_1465, retro_ggor_556,
Myotis lucifugus	ENSMLUG00000001559	30 retrocopies	retro_mluc_1114, retro_mluc_1132, retro_mluc_1165, retro_mluc_1277, retro_mluc_1288, retro_mluc_1418, retro_mluc_1467, retro_mluc_1476, retro_mluc_1486, retro_mluc_1634, retro_mluc_1656, retro_mluc_1689, retro_mluc_1808, retro_mluc_1911, retro_mluc_1938, retro_mluc_2043, retro_mluc_2055, retro_mluc_2085, retro_mluc_2111, retro_mluc_2153, retro_mluc_2182, retro_mluc_2209, retro_mluc_2414, retro_mluc_460, retro_mluc_662, retro_mluc_730, retro_mluc_773, retro_mluc_820, retro_mluc_821, retro_mluc_906,
Macaca mulatta	ENSMMUG00000015270	2 retrocopies	retro_mmul_275, retro_mmul_70,
Nomascus leucogenys	ENSNLEG00000014147	1 retrocopy	retro_nleu_34,
Oryctolagus cuniculus	ENSOCUG00000012476	1 retrocopy	retro_ocun_168,
Otolemur garnettii	ENSOGAG00000006922	16 retrocopies	retro_ogar_1156, retro_ogar_1746, retro_ogar_1895, retro_ogar_2501, retro_ogar_2529, retro_ogar_2556, retro_ogar_2699, retro_ogar_2723, retro_ogar_2947, retro_ogar_308, retro_ogar_3291, retro_ogar_3436, retro_ogar_394, retro_ogar_521, retro_ogar_730, retro_ogar_805,
Pongo abelii	ENSPPYG00000001426	1 retrocopy	retro_pabe_147,
Pan troglodytes	ENSPTRG00000000659	1 retrocopy	retro_ptro_30,
Pteropus vampyrus	ENSPVAG00000009859	10 retrocopies	retro_pvam_1285, retro_pvam_1315, retro_pvam_1345, retro_pvam_403, retro_pvam_419, retro_pvam_463, retro_pvam_514, retro_pvam_578, retro_pvam_685, retro_pvam_991,
Rattus norvegicus	ENSRNOG00000018768	2 retrocopies	retro_rnor_222, retro_rnor_235,