RetrogeneDB ID: retro_cpor_760

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_263:236219..236500(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000009834
• Aliases: None
• Description: None

Sequence

>retro_cpor_760
AGTGCAATCAATTCTTTCCAGTTCAGATGTAACACTGGGATCATCAATTCTCCCAAGATGATCATTACAAAGTTTCTCAA
CAGCACCTTGTCACAGAAGTTAGATAACCCTCCCAGAAATAGGGTTGCTCACAATCCTCTGACACTTGTCCTTGGCCATA
TGCTCAGTGGGTGGAATGCTTGGCTCTTTTTCCCCTGGATTCTGCCAGTAGATTTGGCAGGCAAAACTCCATGCTAATGG
TCAACATCCTGGTCATGGCCAATGGCTGCTTCATGGGCTTC

Alignment

ORF - retro_cpor_760 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 59.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAIGSFQFGYNTGVINAPEMITTEFINSTLSQKLGNPPSKE-LLTTLWSLSVAIFSVGGM-LGSFSIGLS
          .AI.SFQF..NTG.IN.P.MI.T.F.NSTLSQKL.NPP....LLT.L..LS.AI.SVGGM.L..F....S
Retrocopy SAINSFQFRCNTGIINSPKMIITKFLNSTLSQKLDNPPRNR>LLTIL*HLSLAICSVGGM>LALFPLD-S

Parental  VNHFGRRNSMLMVNVLVVVSGCLMGF
          ...FGR.NSMLMVN.LV...GC.MGF
Retrocopy ASRFGRQNSMLMVNILVMANGCFMGF

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP040447_lung	0.00 RPM	0.03 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.00 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_760 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_760 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004556	2 retrocopies	retro_btau_708, retro_btau_709,
Callithrix jacchus	ENSCJAG00000018988	1 retrocopy	retro_cjac_446,
Cavia porcellus	ENSCPOG00000003074	1 retrocopy	retro_cpor_761,
Cavia porcellus	ENSCPOG00000009834	1 retrocopy	retro_cpor_760 ,
Cavia porcellus	ENSCPOG00000011295	1 retrocopy	retro_cpor_587,
Felis catus	ENSFCAG00000001625	1 retrocopy	retro_fcat_1924,
Homo sapiens	ENSG00000059804	2 retrocopies	retro_hsap_3983, retro_hsap_401,
Gorilla gorilla	ENSGGOG00000016813	1 retrocopy	retro_ggor_398,
Macaca mulatta	ENSMMUG00000000439	2 retrocopies	retro_mmul_2301, retro_mmul_502,
Nomascus leucogenys	ENSNLEG00000026903	2 retrocopies	retro_nleu_1572, retro_nleu_1904,
Oryctolagus cuniculus	ENSOCUG00000008575	1 retrocopy	retro_ocun_352,
Pongo abelii	ENSPPYG00000004234	1 retrocopy	retro_pabe_3274,
Pongo abelii	ENSPPYG00000004235	1 retrocopy	retro_pabe_315,
Pan troglodytes	ENSPTRG00000004624	1 retrocopy	retro_ptro_2703,
Pan troglodytes	ENSPTRG00000004626	1 retrocopy	retro_ptro_307,