RetrogeneDB ID: retro_cpor_1450

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_86:1779953..1780447(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CASP3
• Ensembl ID: ENSCPOG00000012511
• Aliases: None
• Description: None

Sequence

>retro_cpor_1450
GCAACATCCATTAAAAATTTAGAAACAAAGATCGTACATGGAAGCAAATCAATGGACTCCGGAATATTTTTGGACAATAG
ATACAAAATGGATTATCCTGGAATGGGTTTATATTGAGTAATTAATAATAATAATGTTCATAAAAGCTCTGGATGGCAGC
TCAGTCCGGTACAGACATAGATGCAGCAAGCATCAGAGAAACATTTATGAACTGGAAATACAAAGAGAGGGATAAAAATG
ATCTTACATGTGAAGAAATAGTGGAATTGGTATGCAAGATGTCTAAAGAAGATCATAGCAAAAAGGAGCAGGTTGGTTTG
TGTAATTCTAAGCCATGGTGAAGAAGGAAAATCTTCTGGAACAAATGGACCTGTTGACCTGAAAAGAGTAACAAAGTCCT
TCAGAGGGATCTTTGTGGAAGGCTAGCTGGAAAATCCAAATTTTTCATTATTCAGTCTTGCTGGGGCAGGGAACTGCACT
GTGGCATTGAGACA

Alignment

ORF - retro_cpor_1450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 81.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AKSIKNLETKVIHGSKSMDSGIFLDNRYKMDYPEMGLCIVINNKNFHKSTG-MAPRLGTDVDAASIRETF
          A.SIKNLETK..HGSKSMDSGIFLDNRYKMDYP.MGL..VINN.N.HKS.G.MA...GTD.DAASIRETF
Retrocopy ATSIKNLETKIVHGSKSMDSGIFLDNRYKMDYPGMGLY*VINNNNVHKSSG<MAAQSGTDIDAASIRETF

Parental  MNLKYEVRNKNDLSCEEIMNLMYSVSKEDHS-KRSSFVCVILSHGEEGKIFGTNGPVDLKRLTKFFRG-D
          MN.KY..R.KNDL.CEEI..L....SKEDHS.KRS..VCVILSHGEEGK..GTNGPVDLKR.TK.FRG.D
Retrocopy MNWKYKERDKNDLTCEEIVELVCKMSKEDHS>KRSRLVCVILSHGEEGKSSGTNGPVDLKRVTKSFRG<D

Parental  LCRSLTGKPKLFIIQACRGTELDCGIET
          LC..L.GK.K.FIIQ.C.G.EL.CGIET
Retrocopy LCGRLAGKSKFFIIQSCWGRELHCGIET

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	2.65 RPM
SRP017611_kidney	0.00 RPM	2.62 RPM
SRP017611_liver	0.00 RPM	6.49 RPM
SRP040447_lung	0.00 RPM	4.11 RPM
SRP040447_skeletal_muscle	0.12 RPM	1.38 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1450 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1450 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012511	2 retrocopies	retro_cpor_1203, retro_cpor_1450 ,
Dasypus novemcinctus	ENSDNOG00000013931	1 retrocopy	retro_dnov_1013,
Microcebus murinus	ENSMICG00000004809	2 retrocopies	retro_mmur_1389, retro_mmur_691,
Macaca mulatta	ENSMMUG00000012053	1 retrocopy	retro_mmul_114,
Otolemur garnettii	ENSOGAG00000005985	2 retrocopies	retro_ogar_1756, retro_ogar_3263,
Rattus norvegicus	ENSRNOG00000010475	1 retrocopy	retro_rnor_2747,
Sarcophilus harrisii	ENSSHAG00000009178	1 retrocopy	retro_shar_404,
Ictidomys tridecemlineatus	ENSSTOG00000003865	2 retrocopies	retro_itri_172, retro_itri_586,