RetrogeneDB ID: retro_cpor_988

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_38:3976889..3977786(-)
• Located in intron of: ENSCPOG00000009875

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000012328
• Aliases: None
• Description: None

Sequence

>retro_cpor_988
GCCATGGCGATGAGCAGCAGCGGCGATGGTGGCTGCGTCCCAGAGCAGGAAAACTCGGTGCTGTTTCGGCGCGGGACAGG
CCAGAGTGATGACTCTGACATTTGGGATGATACAGCATTGATAAAAGCTTATGATAAAGCTGTGGCTTCCTTTAAGTACG
CTCTAAAGAATGGTGACATTTCAGATAAACCACAAGGAGAAATGTCCGGCAAACCGAAGGGCACACCCAGAAGAAAACCT
GTTAAGAAGAGTAAAAGCCAGAAGAAGAATACCACAGCTCCCTCAAAACAGTGGAAAGTGGGTGACAGGTGTTCTGCTGT
TTGGTCAGAAGATGGCTGCATTTATCCAGCTACAATCGCTTCTGTGGATTTGAAGAGAGAAACCTGTGTTGTGGTCTATA
CTGGATATGGAAACAGGGAGGAACAAAATCTGTCTGATCTACTTTCCCCAAGCTCTGAAGCAGCCAACAACATGGAACAG
AACACGCAGGAGAATGAAAATGGAAGTCAAGTTTCAACGGATGAAAGTGAGAACTCTTCCAAGTCTCCAGGAAGCAAACC
AAGTACGGTCAGGTCGAAAGCCACACCCTGGAACTCCTTTTTCCCTCCGCCACCACCCCCCGTTCCTAGCTCAGGATCTG
GACCTGGAAAGCCAGGTCTAAAATTCAGTGGCCTACCCCCACCCCCACCACCTCCACACTTCCTGTCATGCTGGCTGCCT
CCATTTCCGGCTGGACCTCCAATGATCCCCCCGCCGCCTCCCATCTGTCCAGACTCGTTTGATGATGCAGACGCACTGGG
CAGCATGCTGATGTCGTGGTACATGAGTGGCTATCACACTGGCTACTACATGGGTTTCAGACAAAATCAAAAAGAAGGGA
GGAGCTCACATTTTAAT

Alignment

ORF - retro_cpor_988 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 97.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AMAMSSSGDGGCVPEQENSVLFRRGTGQSDDSDIWDDTALIKAYDKAVASFKYALKNGDISDKPQGEMSG
          AMAMSSSGDGGCVPEQENSVLFRRGTGQSDDSDIWDDTALIKAYDKAVASFKYALKNGDISDKPQGEMSG
Retrocopy AMAMSSSGDGGCVPEQENSVLFRRGTGQSDDSDIWDDTALIKAYDKAVASFKYALKNGDISDKPQGEMSG

Parental  KPKGTPRRKPVKKSKSQKKNTTAPSKQWKVGDRCSAVWSEDGCIYPATIASVDLKRETCVVVYTGYGNRE
          KPKGTPRRKPVKKSKSQKKNTTAPSKQWKVGDRCSAVWSEDGCIYPATIASVDLKRETCVVVYTGYGNRE
Retrocopy KPKGTPRRKPVKKSKSQKKNTTAPSKQWKVGDRCSAVWSEDGCIYPATIASVDLKRETCVVVYTGYGNRE

Parental  EQNLSDLLSPSSEAANNMEQNTQENENGSQVSTDESENSSKSPGSKPSTVRSKATPWNSFFPPPPPPVPS
          EQNLSDLLSPSSEAANNMEQNTQENENGSQVSTDESENSSKSPGSKPSTVRSKATPWNSFFPPPPPPVPS
Retrocopy EQNLSDLLSPSSEAANNMEQNTQENENGSQVSTDESENSSKSPGSKPSTVRSKATPWNSFFPPPPPPVPS

Parental  SGSGPGKPGLKFSGLPPPPPPPHFLSCWLPPFPAGPPMIPPPPPICPDSFDDADALGSMLMSWYMSGYHT
          SGSGPGKPGLKFSGLPPPPPPPHFLSCWLPPFPAGPPMIPPPPPICPDSFDDADALGSMLMSWYMSGYHT
Retrocopy SGSGPGKPGLKFSGLPPPPPPPHFLSCWLPPFPAGPPMIPPPPPICPDSFDDADALGSMLMSWYMSGYHT

Parental  GYYMGFRQNQKEGRSSHFN
          GYYMGFRQNQKEGRSSHFN
Retrocopy GYYMGFRQNQKEGRSSHFN

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	0.40 RPM	4.49 RPM
SRP017611_kidney	0.63 RPM	3.25 RPM
SRP017611_liver	0.70 RPM	2.48 RPM
SRP040447_lung	1.01 RPM	8.37 RPM
SRP040447_skeletal_muscle	0.26 RPM	4.62 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_988 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_988 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 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012328	1 retrocopy	retro_cpor_988 ,
Dasypus novemcinctus	ENSDNOG00000007283	4 retrocopies	retro_dnov_1239, retro_dnov_1613, retro_dnov_1637, retro_dnov_2175,
Echinops telfairi	ENSETEG00000001406	2 retrocopies	retro_etel_1549, retro_etel_2012,
Homo sapiens	ENSG00000205571	1 retrocopy	retro_hsap_4140,
Gorilla gorilla	ENSGGOG00000026704	1 retrocopy	retro_ggor_2780,
Myotis lucifugus	ENSMLUG00000010603	1 retrocopy	retro_mluc_1623,
Macaca mulatta	ENSMMUG00000020214	1 retrocopy	retro_mmul_216,
Nomascus leucogenys	ENSNLEG00000004454	1 retrocopy	retro_nleu_1054,
Oryctolagus cuniculus	ENSOCUG00000017097	1 retrocopy	retro_ocun_617,
Pan troglodytes	ENSPTRG00000016955	1 retrocopy	retro_ptro_2813,
Sus scrofa	ENSSSCG00000016970	1 retrocopy	retro_sscr_654,
Ictidomys tridecemlineatus	ENSSTOG00000012288	1 retrocopy	retro_itri_968,
Tupaia belangeri	ENSTBEG00000002399	1 retrocopy	retro_tbel_1033,