RetrogeneDB ID: retro_cpor_353

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_13:36298181..36298587(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX4
• Ensembl ID: ENSCPOG00000004185
• Aliases: None
• Description: None

Sequence

>retro_cpor_353
GCAAATCCATCACCTTATTGGGGAGGAACAGCTGTGATACATGGAGAATTCAAGGAGCTGAAATTAACTGGTTATCGTGG
AAAATACTTGGTTTTTTTTTTCTATCCACTTGATTTCACATTTGTGTGTCCAACTGAAATGATGACTTATGGTGACAGAA
CTGAAGAACTCAGATCTATAGAAACCAAGGTGGTGCTGTGTTCTGGCAATCCACAGTCTGCCTGTCTGACCCGGTTTGAT
GCTTCGGAGACTAGGAGGACTGGGGCCCATAATGATCCCGCTGTGTCAGACCTGGGCCATTGGATCCCAGAGAACTGGAT
GTGTATCCAGAGGCCGCAGACCACACCCTGAAAGCCTTGTGTTTACTGATGACAGAGGACTCCTGAGACCCAGGACTCAG
CCTGAC

Alignment

ORF - retro_cpor_353 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.8 %
• Parental protein coverage: 50.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SKPAPYWEGTAVINGEFKELKLTDYRGKYLVFFFYPLDFTFVCPTEIIAFGDRIEEFRAINTEVVACSVD
          ..P.PYW.GTAVI.GEFKELKLT.YRGKYL....YPLDFTFVCPTE....GDR.EE.R.I.T.VV.CS..
Retrocopy ANPSPYWGGTAVIHGEFKELKLTGYRGKYLXXXXYPLDFTFVCPTEMMTYGDRTEELRSIETKVVLCSGN

Parental  SQFTHLAWINTPRRQGGLGSIKIPLLSDLNHQISKDY-GVYLEDAGHTLRGLFII-DDKGILRQITLND
          .Q...L............G....P..SDL.H.I......VY.E.A.HTL..L....DD.G.LR..T..D
Retrocopy PQSACLTRFDASETR-RTGAHNDPAVSDLGHWIPENW<DVYPEAADHTLKALCLL<DDRGLLRPRTQPD

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	0.12 RPM	9.78 RPM
SRP017611_kidney	0.00 RPM	27.74 RPM
SRP017611_liver	0.00 RPM	34.60 RPM
SRP040447_lung	0.05 RPM	29.41 RPM
SRP040447_skeletal_muscle	0.01 RPM	12.28 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_353 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_353 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 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006165	1 retrocopy	retro_btau_439,
Cavia porcellus	ENSCPOG00000004185	1 retrocopy	retro_cpor_353 ,
Cavia porcellus	ENSCPOG00000014137	3 retrocopies	retro_cpor_1079, retro_cpor_290, retro_cpor_398,
Equus caballus	ENSECAG00000010085	1 retrocopy	retro_ecab_576,
Homo sapiens	ENSG00000123131	1 retrocopy	retro_hsap_3165,
Gorilla gorilla	ENSGGOG00000026790	1 retrocopy	retro_ggor_1351,
Myotis lucifugus	ENSMLUG00000004904	2 retrocopies	retro_mluc_2347, retro_mluc_2619,
Macaca mulatta	ENSMMUG00000021366	1 retrocopy	retro_mmul_2001,
Tupaia belangeri	ENSTBEG00000004454	5 retrocopies	retro_tbel_2164, retro_tbel_2467, retro_tbel_2522, retro_tbel_2811, retro_tbel_2978,
Tarsius syrichta	ENSTSYG00000000602	1 retrocopy	retro_tsyr_404,
Tursiops truncatus	ENSTTRG00000012368	1 retrocopy	retro_ttru_547,