RetrogeneDB ID: retro_cpor_1071

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_43:9097305..9097634(-)
• Located in intron of: ENSCPOG00000000776

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRP14
• Ensembl ID: ENSCPOG00000008994
• Aliases: None
• Description: None

Sequence

>retro_cpor_1071
ATGGTGCTGCTGGAGAGCAAGCAGTTGCTGACTGAGCTGACCATGCTCCTCCAGAAGTGCCAGATGCAGGGCAGTGTGTT
CGTCACCTGAGAAAATACGATGGTCGAGCTAGCTGCATCCCAAAAAAGGGTTCTGGGGAGCACTTTGAGCCTTCAGATTC
CAAACGTCTGTTGAGAGCTGCGGATTGGGGAAAAGGAGATCAACACTGCGGTGAGCTCCAAAGACGTGATGTGTTTCTGA
TGGCTTATTCCAGCGTGTTGAGAGCTCGCAGGAGAGGGCCGAAGAAGGGAGACTGAAACAACCAGAATCCAAAGGCCAAA
ACGGCACAG

Alignment

ORF - retro_cpor_1071 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.6 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVLLESEQFLTELTRLFQKCRTSGSVFIT-LKKYDGRTRSIPKKGTVEGFEPSDNKCLLRATD-GKKKIS
          MVLLES.Q.LTELT.L.QKC...GSVF.T.L.KYDGR...IPKKG..E.FEPSD.K.LLRA.D.G.K.I.
Retrocopy MVLLESKQLLTELTMLLQKCQMQGSVFVT<LRKYDGRASCIPKKGSGEHFEPSDSKRLLRAAD>GEKEIN

Parental  TVVSSKEV-NKFQMAYSNLLRANMDGLKKRDKKNKNKKAKTAQ
          T.VSSK.V...F.MAYS..LRA...G.KK.D..N.N.KAKTAQ
Retrocopy TAVSSKDV<DVFLMAYSSVLRARRRGPKKGD*NNQNPKAKTAQ

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	27.21 RPM
SRP017611_kidney	0.00 RPM	27.74 RPM
SRP017611_liver	0.00 RPM	18.32 RPM
SRP040447_lung	0.03 RPM	25.70 RPM
SRP040447_skeletal_muscle	0.00 RPM	28.52 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1071 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1071 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 20 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029889	2 retrocopies	retro_cfam_210, retro_cfam_40,
Choloepus hoffmanni	ENSCHOG00000005321	2 retrocopies	retro_chof_212, retro_chof_2659,
Callithrix jacchus	ENSCJAG00000020912	3 retrocopies	retro_cjac_1642, retro_cjac_171, retro_cjac_3057,
Cavia porcellus	ENSCPOG00000008994	2 retrocopies	retro_cpor_1071 , retro_cpor_462,
Dasypus novemcinctus	ENSDNOG00000011147	3 retrocopies	retro_dnov_1303, retro_dnov_2164, retro_dnov_2599,
Echinops telfairi	ENSETEG00000011870	1 retrocopy	retro_etel_1094,
Homo sapiens	ENSG00000140319	3 retrocopies	retro_hsap_1765, retro_hsap_811, retro_hsap_949,
Gorilla gorilla	ENSGGOG00000009921	1 retrocopy	retro_ggor_665,
Myotis lucifugus	ENSMLUG00000010531	5 retrocopies	retro_mluc_1489, retro_mluc_2284, retro_mluc_2545, retro_mluc_375, retro_mluc_384,
Macaca mulatta	ENSMMUG00000016061	4 retrocopies	retro_mmul_1228, retro_mmul_1740, retro_mmul_573, retro_mmul_780,
Monodelphis domestica	ENSMODG00000029204	1 retrocopy	retro_mdom_1806,
Mustela putorius furo	ENSMPUG00000008324	1 retrocopy	retro_mputfur_376,
Nomascus leucogenys	ENSNLEG00000002457	2 retrocopies	retro_nleu_246, retro_nleu_2831,
Otolemur garnettii	ENSOGAG00000029070	2 retrocopies	retro_ogar_2839, retro_ogar_40,
Pongo abelii	ENSPPYG00000006342	3 retrocopies	retro_pabe_1534, retro_pabe_262, retro_pabe_811,
Pan troglodytes	ENSPTRG00000006911	3 retrocopies	retro_ptro_1181, retro_ptro_564, retro_ptro_656,
Tupaia belangeri	ENSTBEG00000016637	1 retrocopy	retro_tbel_196,
Tarsius syrichta	ENSTSYG00000009467	4 retrocopies	retro_tsyr_1283, retro_tsyr_1985, retro_tsyr_60, retro_tsyr_73,
Tursiops truncatus	ENSTTRG00000000036	5 retrocopies	retro_ttru_1185, retro_ttru_1288, retro_ttru_594, retro_ttru_74, retro_ttru_782,
Vicugna pacos	ENSVPAG00000010282	1 retrocopy	retro_vpac_20,