RetrogeneDB ID: retro_cpor_1175

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_52:8448831..8449109(-)
• Located in intron of: ENSCPOG00000005288

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS23
• Ensembl ID: ENSCPOG00000008761
• Aliases: None
• Description: None

Sequence

>retro_cpor_1175
GAGGCCTTCTGCCCCAAGGAGCTGGTCTTCCACAGGTTCTTCTCGGGATGCTGCAAAGCCAAAGTGCCCATCCAGGACAC
CTTGTACCATAGGAATCCAATTAGAGCAAAAATTTATCTGTTTATGAATCTGGTCAAAAAGCCTTTGATCTGCTCAATCC
AAACTTCAAGTTTACCTCTCAGCAGTTTATGGAGAAGTACGTTGAGCCACACAATCTTGGAGAAACAAAAGTTATTTATG
GAAACAGGAAAGGTTTACTGATAGAAGGTGGCATTTTA

Alignment

ORF - retro_cpor_1175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.14 %
• Parental protein coverage: 53.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EAFPPLREPVFQRPRLRYGKAKAPIQDILYHEDRIRAKFY-SAYGPGQKAFDLFNPNFRSTCQRFVEKYI
          EAF.P..E.VF.R......KAK.PIQD.LYH...IRAK.Y.S.Y..GQKAFDL.NPNF..T.Q.F.EKY.
Retrocopy EAFCP-KELVFHRFFSGCCKAKVPIQDTLYHRNPIRAKIY<SVYESGQKAFDLLNPNFKFTSQQFMEKYV

Parental  ELQNLGETDEEKLFVETGKSLLAEGVIL
          E..NLGET...K......K.LL.EG.IL
Retrocopy EPHNLGET---KVIYGNRKGLLIEGGIL

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	9.26 RPM
SRP017611_kidney	0.00 RPM	16.33 RPM
SRP017611_liver	0.00 RPM	15.93 RPM
SRP040447_lung	0.00 RPM	10.52 RPM
SRP040447_skeletal_muscle	0.01 RPM	24.32 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1175 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1175 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014008	1 retrocopy	retro_cjac_3047,
Cavia porcellus	ENSCPOG00000008761	1 retrocopy	retro_cpor_1175 ,
Felis catus	ENSFCAG00000005711	1 retrocopy	retro_fcat_963,
Homo sapiens	ENSG00000181610	1 retrocopy	retro_hsap_3727,
Macaca mulatta	ENSMMUG00000001913	1 retrocopy	retro_mmul_1691,
Mustela putorius furo	ENSMPUG00000015372	1 retrocopy	retro_mputfur_1274,
Nomascus leucogenys	ENSNLEG00000008072	1 retrocopy	retro_nleu_1972,
Pongo abelii	ENSPPYG00000025941	1 retrocopy	retro_pabe_3131,
Pan troglodytes	ENSPTRG00000009440	1 retrocopy	retro_ptro_2523,
Tarsius syrichta	ENSTSYG00000009862	1 retrocopy	retro_tsyr_2077,