RetrogeneDB ID: retro_cpor_1243

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_6:3112062..3112532(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSR3
• Ensembl ID: ENSCPOG00000005898
• Aliases: None
• Description: None

Sequence

>retro_cpor_1243
TCTTCTGTGCTCTTCTTTGAGAATGCATTCATCACATCTGCCATCTCCATCTGGTTATATTACTGAATATGACACATGGA
TCTTATTCAATCTGCTGTTCTGTATCATGAAATGATCTTGGTAAGCACTTATTTGGTAGCCTTTGTATTCAAGAATGTAA
AAACTGTTCTCAAGCACAGAATAGCAAAGTGGGAGAATGCTGTTTCCAAAGAAGTGACTGGGCAACGTTATGAAGCTAAT
TATAGAAAGATGCCTCAGAATGAGAAAGATGAAAGAATCTTGTGGAAAAAGAATGAAGTTTCTGATTATGAAGCTACAAC
ATTTGCCATCTTTTATAACAACATCTTGTTCTGGCCTTGGTTATTGTTGCTTCCTTCTTTATATTGGAGAATTTCAACTA
CACAGTGAACTACATTTTTTCCATAAGTACTTCATCAGGACGCATCACCATCCTCTCAACTGGTTCCAAG

Alignment

ORF - retro_cpor_1243 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.84 %
• Parental protein coverage: 85.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSALFFGNAFIVSAIPIWLYWRIWHMDLIQSAVLYSVMTLVSTYLVAFAYKNVKFVLKHKVAQKREDAVS
          SS.LFF.NAFI.SAI.IWLY..I.HMDLIQSAVLY..M.LVSTYLVAF..KNVK.VLKH..A.K.E.AVS
Retrocopy SSVLFFENAFITSAISIWLYY*I*HMDLIQSAVLYHEMILVSTYLVAFVFKNVKTVLKHRIA-KWENAVS

Parental  KEVTRKLSEADNRRMSRKEKDERILWKKNEVADYEATTFSIFYNNTLF-LVLVIVASFFILKNFNPTVNY
          KEVT....EA..R.M...EKDERILWKKNEV.DYEATTF.IFYNN.LF.L.LVIVASFFIL.NFN.TVNY
Retrocopy KEVTGQRYEANYRKMPQNEKDERILWKKNEVSDYEATTFAIFYNNILF<LALVIVASFFILENFNYTVNY

Parental  ILSISASSGLIALLSTGSK
          I.SIS.SSG.I..LSTGSK
Retrocopy IFSISTSSGRITILSTGSK

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	29.68 RPM
SRP017611_kidney	0.00 RPM	37.90 RPM
SRP017611_liver	0.00 RPM	43.18 RPM
SRP040447_lung	0.00 RPM	58.56 RPM
SRP040447_skeletal_muscle	0.00 RPM	57.36 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1243 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1243 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 14 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003125	1 retrocopy	retro_amel_832,
Canis familiaris	ENSCAFG00000008870	5 retrocopies	retro_cfam_1296, retro_cfam_1370, retro_cfam_1924, retro_cfam_2029, retro_cfam_2041,
Choloepus hoffmanni	ENSCHOG00000001517	1 retrocopy	retro_chof_29,
Callithrix jacchus	ENSCJAG00000004643	4 retrocopies	retro_cjac_1059, retro_cjac_1503, retro_cjac_2369, retro_cjac_3213,
Cavia porcellus	ENSCPOG00000005898	2 retrocopies	retro_cpor_1243 , retro_cpor_826,
Dasypus novemcinctus	ENSDNOG00000000752	2 retrocopies	retro_dnov_1922, retro_dnov_632,
Homo sapiens	ENSG00000114850	1 retrocopy	retro_hsap_173,
Gorilla gorilla	ENSGGOG00000024038	1 retrocopy	retro_ggor_255,
Myotis lucifugus	ENSMLUG00000015478	3 retrocopies	retro_mluc_1624, retro_mluc_1728, retro_mluc_2146,
Macaca mulatta	ENSMMUG00000016970	1 retrocopy	retro_mmul_383,
Otolemur garnettii	ENSOGAG00000010589	2 retrocopies	retro_ogar_2089, retro_ogar_3483,
Pongo abelii	ENSPPYG00000014233	1 retrocopy	retro_pabe_456,
Pan troglodytes	ENSPTRG00000015560	1 retrocopy	retro_ptro_163,
Tarsius syrichta	ENSTSYG00000010578	1 retrocopy	retro_tsyr_660,