RetrogeneDB ID: retro_cpor_1139

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_5:41746352..41746683(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS7
• Ensembl ID: ENSCPOG00000009795
• Aliases: None
• Description: None

Sequence

>retro_cpor_1139
GAAACTATCATCACTTTTGTTCCAGGTCCCCAGCTGAAATCTTTCCAGAAACTCTGGTTGGGCTAGACCAAGAGCTGGAG
AAGGATCTGAGCGGGAAGCCTGTGGTCTCCGCGGCACAGAGGAGAATTCCACCTAAGCCAACCTGGAAAAGCCGCACAAA
GAAGTAAGCAGAAGCGTCCCGGAGCTGCACACTGACTGCTGTGCACGACGCCGTCCTGGAGGACCTGGTTTCTCCTATCG
AGATCGCGGGCAAGAGAACTGGCGTGAAGCTGGAGGGCCGCGGGCTCACCAGGGTGCACCTGAGCAAGGCCAGCAGAGCA
ACGCCGAGCAT

Alignment

ORF - retro_cpor_1139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.1 %
• Parental protein coverage: 57.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KAIIIFVPVPQLKSFQKIQ-VRLVRELEKKFSGKHVVFIAQQRRILPKPTRKSRTK-NKQKRP-RSRTLT
          ..II.FVP.PQLKSFQK...V.L..ELEK..SGK.VV..AQ.RRI.PKPT.KSRTK..KQKRP.RS.TLT
Retrocopy ETIITFVPGPQLKSFQKLW<VGLDQELEKDLSGKPVVSAAQ-RRIPPKPTWKSRTK>SKQKRP<RSCTLT

Parental  AVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKA-QQNNVEH
          AVHDA.LEDLV.P.EI.GKR..VKL.G..L..VHL.KA.QQ.N.EH
Retrocopy AVHDAVLEDLVSPIEIAGKRTGVKLEGRGLTRVHLSKA<QQSNAEH

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	121.99 RPM
SRP017611_kidney	0.00 RPM	231.57 RPM
SRP017611_liver	0.00 RPM	142.68 RPM
SRP040447_lung	0.00 RPM	278.94 RPM
SRP040447_skeletal_muscle	0.00 RPM	318.25 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1139 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1139 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 66 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016224	5 retrocopies	retro_btau_1016, retro_btau_1046, retro_btau_1351, retro_btau_448, retro_btau_997,
Canis familiaris	ENSCAFG00000003263	1 retrocopy	retro_cfam_1798,
Callithrix jacchus	ENSCJAG00000016462	2 retrocopies	retro_cjac_16, retro_cjac_2287,
Cavia porcellus	ENSCPOG00000009795	2 retrocopies	retro_cpor_1139 , retro_cpor_773,
Felis catus	ENSFCAG00000023243	2 retrocopies	retro_fcat_1534, retro_fcat_41,
Gorilla gorilla	ENSGGOG00000023095	13 retrocopies	retro_ggor_2028, retro_ggor_2090, retro_ggor_2161, retro_ggor_218, retro_ggor_2452, retro_ggor_2927, retro_ggor_294, retro_ggor_2965, retro_ggor_3047, retro_ggor_346, retro_ggor_400, retro_ggor_484, retro_ggor_597,
Loxodonta africana	ENSLAFG00000015087	11 retrocopies	retro_lafr_1223, retro_lafr_160, retro_lafr_217, retro_lafr_318, retro_lafr_319, retro_lafr_413, retro_lafr_514, retro_lafr_720, retro_lafr_786, retro_lafr_964, retro_lafr_970,
Myotis lucifugus	ENSMLUG00000006121	1 retrocopy	retro_mluc_1118,
Mus musculus	ENSMUSG00000061477	2 retrocopies	retro_mmus_271, retro_mmus_53,
Oryctolagus cuniculus	ENSOCUG00000008507	2 retrocopies	retro_ocun_203, retro_ocun_230,
Otolemur garnettii	ENSOGAG00000028165	1 retrocopy	retro_ogar_133,
Pongo abelii	ENSPPYG00000025872	12 retrocopies	retro_pabe_1033, retro_pabe_1555, retro_pabe_2506, retro_pabe_2982, retro_pabe_2983, retro_pabe_31, retro_pabe_313, retro_pabe_360, retro_pabe_3659, retro_pabe_3803, retro_pabe_499, retro_pabe_524,
Pan troglodytes	ENSPTRG00000011615	3 retrocopies	retro_ptro_202, retro_ptro_3132, retro_ptro_58,
Pteropus vampyrus	ENSPVAG00000002071	7 retrocopies	retro_pvam_1051, retro_pvam_1183, retro_pvam_1330, retro_pvam_1437, retro_pvam_207, retro_pvam_543, retro_pvam_887,
Rattus norvegicus	ENSRNOG00000008551	2 retrocopies	retro_rnor_39, retro_rnor_391,