RetrogeneDB ID: retro_cpor_101

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_79:2109354..2110194(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000025329
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: C16ORF72
• Ensembl ID: ENSCPOG00000010925
• Aliases: None
• Description: None

Sequence

>retro_cpor_101
ATGGAGGGACCGCCGCCGGAGGGAGACGCCGAAGTCTCCGAGCCCTGGTTGTCCAAGTGGGAGCGCCAGTGCCTGGCCGA
GGCCGAGGCCGAGCAGGGCGAGACGCTGCCCCCGGAGCAGCAGGCGGAGGCGACCGCCGAGGCTGAGGGGATCCGCGGCG
AGCTGCAGCGGGTGTGGCACCTCTTCCAGCTCGCCGCCAACGCCGTGGCCCAGCTCTACCAGGACTCGGAGTGCCAGCAG
CCGGAACAGTCCGTGTGGGACCCCTTCCAGAGGGCTGCCATGGCCGTGACCGACCTGTACAAGGAGAGCGGGGACGACGC
TCGCCGCCGCTGTCTGGACCTGGGCGTCCAGGTGGGCTGCCGCCGTCGCGTCGGGGACGTGCTGGAGTGGGCCAAGAAGG
GCCGCAGCACCATCCGCCGCGAAGACCTCATCAGCTTCCTCTGCGGCAAAGCGCCCCCCGAGGCGCCACCGCCGCGCGCC
CCCAGGACGCCCCCGAAGCCACCTGCCGGTGCCGCCGGCCAGGCTGCTGTCACCGAGTCCAACCCCTCTGTGGACGTCGA
CCTGCAGCTCTTCCACGAGGCCGCCGCGCTGCATGGCCTAGATGGCGCTGCGGCGAGCGTCGGCGTGCCAACAGGGGCGC
CCGGCTCCCCGCCCCAAGGCAGCGGTGTCGCCTGCGGTGGGCGCACGCAAAGCAGCTTCCTCGAGGACGACCTGAACCGC
TTCGGCTCAGAAGAACTGGGTCTTCACCTGGACAGTGGGGGTATCCGAAAGCGCCCCTCGACCCAGCTCGGCGACTGCTT
CACAGACTCCCCGTCCCACAAGCGCAACCGAATGGTCTAA

Alignment

ORF - retro_cpor_101 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FQNSATAVAQLYKDRVCQQPGLSLWVPFQNAATAVTNLYKESVD-THQRSFDIGIQIGYQRRNKDVLAWV
          FQ..A.AVAQLY.D..CQQP..S.W.PFQ.AA.AVT.LYKES.D....R..D.G.Q.G..RR..DVL.W.
Retrocopy FQLAANAVAQLYQDSECQQPEQSVWDPFQRAAMAVTDLYKESGDDARRRCLDLGVQVGCRRRVGDVLEWA

Parental  KKRRRTIRREDLISFLCGKV----PPPRNSRAPPRLTVVSPNRATSAETSSSVETDLQPFREAIALHGLS
          KK.R.TIRREDLISFLCGK.....PPPR..R.PP.........A...E...SV..DLQ.F.EA.ALHGL.
Retrocopy KKGRSTIRREDLISFLCGKAPPEAPPPRAPRTPPKPPAGAAGQAAVTESNPSVDVDLQLFHEAAALHGLD

Parental  GAMASISVRSSTPGSPTHVSSGSNASRRRNGLHDVDLNTFISEEMALHLDNGGTRKRTSAQCGDVITDSP
          GA.AS..V....PGSP...S......R........DLN.F.SEE..LHLD.GG.RKR.S.Q.GD..TDSP
Retrocopy GAAASVGVPTGAPGSPPQGSGVACGGRTQSSFLEDDLNRFGSEELGLHLDSGGIRKRPSTQLGDCFTDSP

Parental  THKRNRMI
          .HKRNRM.
Retrocopy SHKRNRMV

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	20.82 RPM
SRP017611_kidney	0.00 RPM	14.55 RPM
SRP017611_liver	0.00 RPM	10.84 RPM
SRP040447_lung	0.00 RPM	20.33 RPM
SRP040447_skeletal_muscle	0.01 RPM	19.00 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_101 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_101 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 17 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010719	2 retrocopies	retro_amel_1715, retro_amel_88,
Canis familiaris	ENSCAFG00000018981	1 retrocopy	retro_cfam_147,
Cavia porcellus	ENSCPOG00000010925	1 retrocopy	retro_cpor_101 ,
Dasypus novemcinctus	ENSDNOG00000015893	3 retrocopies	retro_dnov_1575, retro_dnov_2266, retro_dnov_827,
Equus caballus	ENSECAG00000009430	1 retrocopy	retro_ecab_1091,
Homo sapiens	ENSG00000182831	1 retrocopy	retro_hsap_4765,
Gorilla gorilla	ENSGGOG00000010744	1 retrocopy	retro_ggor_2968,
Monodelphis domestica	ENSMODG00000005378	2 retrocopies	retro_mdom_1716, retro_mdom_299,
Mustela putorius furo	ENSMPUG00000014707	1 retrocopy	retro_mputfur_44,
Mus musculus	ENSMUSG00000022507	1 retrocopy	retro_mmus_3460,
Nomascus leucogenys	ENSNLEG00000010106	1 retrocopy	retro_nleu_2348,
Otolemur garnettii	ENSOGAG00000003909	1 retrocopy	retro_ogar_74,
Pongo abelii	ENSPPYG00000007088	1 retrocopy	retro_pabe_163,
Pan troglodytes	ENSPTRG00000007751	1 retrocopy	retro_ptro_3172,
Rattus norvegicus	ENSRNOG00000002545	2 retrocopies	retro_rnor_156, retro_rnor_1928,
Sus scrofa	ENSSSCG00000028454	1 retrocopy	retro_sscr_1177,
Ictidomys tridecemlineatus	ENSSTOG00000009324	1 retrocopy	retro_itri_137,