RetrogeneDB ID: retro_cpor_462

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_16:1619570..1619798(-)
• Located in intron of: ENSCPOG00000013113

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_462
GATGGCCAAACTAGATCTATCCCAAACAAGGGTTCTGTGGAGGGCTTTGAGCCTCTGGATAACATGTGTCTGTTGAGAGC
TACTCATGGGGAAAAGGTCAGCACTGTAGTGAGCTCCAAAGACATGAGTAAGTTTCAGATGGTTTATTCAGACCTATTGA
GAGCTAACATGGATAGGCTGAAGAAGAAAGGCAAAAAGAACAATAAAGACCAAATCAGCATAGCGCAG

Alignment

ORF - retro_cpor_462 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.83 %
• Parental protein coverage: 70. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DGRTRSIPKKGTVEGFEPSDNKCLLRATDGKKKISTVVSSKEVNKFQMAYSNLLRANMDGLKKRDKKNKN
          DG.TRSIP.KG.VEGFEP.DN.CLLRAT.G.K..STVVSSK...KFQM.YS.LLRANMD.LKK..KKN..
Retrocopy DGQTRSIPNKGSVEGFEPLDNMCLLRATHGEK-VSTVVSSKDMSKFQMVYSDLLRANMDRLKKKGKKNNK

Parental  KKAKTAQ
          .....AQ
Retrocopy DQISIAQ

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	0.00 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_462 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_462 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,