RetrogeneDB ID: retro_cpor_8

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_37:216448..217615(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000000733
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000008652
• Aliases: None
• Description: None

Sequence

>retro_cpor_8
ATGCTCTCCGTCCGTGCCCTGCTCGCCACGCTTGCAGACCAGCAGCAGCTGCAGCTGTCGCCGCTGAAGGGACTCAGCCT
GGCTGACAAGGAGAACACGCCTCCGTCCCTCAGCGGGACTCGCGTGCTGGCCAGTAAGACCGCGCGGCTGATCTTCCAGG
AGCCCACCGAGCCGAAGAGTAAGGGATTTGCGCCCAGCGTGGAGGAGGAACCACTGCTGAGAGAGAACCCCCGGCGCTTT
GTCATCTTCCCTATCGAATACCATGACATTTGGCAGATGTATAAGAAAGCCGAGGCCTCCTTTTGGACGGCAGAGGAGGT
GGATCTTTCCAAAGACATTCAGCACTGGGAAGCCCTGAAGCCCGAGGAGAGATACTTTATATCACACGTTCTGGCTTTCT
TTGCCGCCAGCGATGGCATAGTCAATGAGAATTTGGTGGAGCGGTTCAGCCAAGAAGTTCAAATCACAGAGGCTCGCTGT
TTCTACGGCTTCCAGATCGCCATGGAAAACATTCATTCTGAAATGTACAGTCTCCTCATCGATACTTATATCAAAGATTC
CAGAGAAAGGGAGTTCCTCTTCAATGCCATCGAGACCATGCCCTGTGTGAAGAAGTCGGACTGGGCCTTGCGCTGGATTG
GGGACAAAGAGGCCACTTATGGGGAACGCGTGGTAGCCTTTGCTGCCGTGGAAGGCATCTTTTTTTCTGGTTCTTTTGCG
TCGATCTTCTGGCTGAAGAAACGGGGACTCATGCCCGGCCTCACCTTTTCCAATGAACTCATCAGCAGAGATGAGGGCCT
GCACTGTGACTTCGCCTGCCTGATGTTCAAGCACCTGATGCATAGACCCTCAGAGCAGAGGGTGAAGGAGATTATCGTCA
ACGCCGTCAGAATCGAGCAGGAGTTCCTCACGGAGGCCTTGCCAGTGAAGCTGATTGGCATGAACTGCGAGCTCATGAAG
CAGTACATCGAGTTCGTGGCTGACAGGCTCATGCTAGAGCTGGGCTTTGGCAAGGTTTTTCAAGTGGAAAATCCATTTGA
CTTCATGGAGAATATTTCTCTAGAAGGGAAGACAAACTTCTTTGAGAAGAGGGTAGGCGAGTATCAGAGGATGGGAGTTA
TGTCCAGCCCCACGGAGAATTCTTTCACATTGGATGCTGACTTTTAG

Alignment

ORF - retro_cpor_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MLSVRAPLATLADQQQLQLSPLKGLSLADKENTPPSLSGTRVLASKTARRIFQEPTEPLQQQKSKGFAPS
          MLSVRA.LATLADQQQLQLSPLKGLSLADKENTPPSLSGTRVLASKTAR.IFQEPTEP....KSKGFAPS
Retrocopy MLSVRALLATLADQQQLQLSPLKGLSLADKENTPPSLSGTRVLASKTARLIFQEPTEP----KSKGFAPS

Parental  VEEEPLLRENPRRFVIFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEALKPEERYFISHVLAFFAA
          VEEEPLLRENPRRFVIFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEALKPEERYFISHVLAFFAA
Retrocopy VEEEPLLRENPRRFVIFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEALKPEERYFISHVLAFFAA

Parental  SDGIVNENLVERFSQEVQITEARCFYGFQIAMENIHSEMYSLLIDTYIKDSREREFLFNAIETMPCVKKK
          SDGIVNENLVERFSQEVQITEARCFYGFQIAMENIHSEMYSLLIDTYIKDSREREFLFNAIETMPCVKK.
Retrocopy SDGIVNENLVERFSQEVQITEARCFYGFQIAMENIHSEMYSLLIDTYIKDSREREFLFNAIETMPCVKK-

Parental  ADWALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLM
          .DWALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLM
Retrocopy SDWALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLM

Parental  FKHLVHRPSEQRVKEIIVNAVRIEQEFLTEALPVKLIGMNCELMKQYIEFVADRLMLELGFGKVFQVENP
          FKHL.HRPSEQRVKEIIVNAVRIEQEFLTEALPVKLIGMNCELMKQYIEFVADRLMLELGFGKVFQVENP
Retrocopy FKHLMHRPSEQRVKEIIVNAVRIEQEFLTEALPVKLIGMNCELMKQYIEFVADRLMLELGFGKVFQVENP

Parental  FDFMENISLEGKTNFFEKRVGEYQRMGVMSSPTENSFTLDADF
          FDFMENISLEGKTNFFEKRVGEYQRMGVMSSPTENSFTLDADF
Retrocopy FDFMENISLEGKTNFFEKRVGEYQRMGVMSSPTENSFTLDADF

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	0.06 RPM	1.32 RPM
SRP017611_kidney	0.00 RPM	1.15 RPM
SRP017611_liver	0.00 RPM	0.83 RPM
SRP040447_lung	0.25 RPM	4.77 RPM
SRP040447_skeletal_muscle	0.01 RPM	0.80 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_8 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_8 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 18 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003409	1 retrocopy	retro_cfam_2113,
Callithrix jacchus	ENSCJAG00000006533	3 retrocopies	retro_cjac_2134, retro_cjac_2950, retro_cjac_3851,
Cavia porcellus	ENSCPOG00000008652	1 retrocopy	retro_cpor_8 ,
Erinaceus europaeus	ENSEEUG00000009755	2 retrocopies	retro_eeur_421, retro_eeur_585,
Echinops telfairi	ENSETEG00000015797	2 retrocopies	retro_etel_640, retro_etel_691,
Homo sapiens	ENSG00000171848	1 retrocopy	retro_hsap_4815,
Macropus eugenii	ENSMEUG00000000121	3 retrocopies	retro_meug_1450, retro_meug_199, retro_meug_277,
Microcebus murinus	ENSMICG00000012789	1 retrocopy	retro_mmur_1384,
Myotis lucifugus	ENSMLUG00000010596	1 retrocopy	retro_mluc_794,
Macaca mulatta	ENSMMUG00000002057	1 retrocopy	retro_mmul_2568,
Monodelphis domestica	ENSMODG00000014763	1 retrocopy	retro_mdom_775,
Mus musculus	ENSMUSG00000020649	2 retrocopies	retro_mmus_2472, retro_mmus_3073,
Nomascus leucogenys	ENSNLEG00000013733	2 retrocopies	retro_nleu_2190, retro_nleu_3040,
Otolemur garnettii	ENSOGAG00000007075	1 retrocopy	retro_ogar_2665,
Pongo abelii	ENSPPYG00000012656	1 retrocopy	retro_pabe_3743,
Rattus norvegicus	ENSRNOG00000023272	1 retrocopy	retro_rnor_331,
Sus scrofa	ENSSSCG00000021742	1 retrocopy	retro_sscr_901,
Tursiops truncatus	ENSTTRG00000017209	1 retrocopy	retro_ttru_603,