RetrogeneDB ID: retro_cpor_1203

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_56:10587272..10587584(+)
• 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_1203
TTACATGGAAGTAAATCCGTTAACTCTGGAATATTCTTGGATAATGGATTCGAAATGAGTTATTCTGAAATGGGCTTATG
TACAGTAATAAATAAGAAGAACTTTCATTAGAGCACTGGAATGACAGCTTGGTCTGATACAGATGTAGATGCAGCAAACA
TTAGAGAAATATTAATAAACTTCAACTATGAATTGAGGAATAAAAATGATCTTACATGTGAAAAAATAATGGAATTAATA
AGCAAAATTCCTAAAGAAGACCATAGTAAAACGAGCAGCATTGTTTGCATAATGCTAAGCCATCGTCAAGAA

Alignment

ORF - retro_cpor_1203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.42 %
• Parental protein coverage: 51.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IHGSKSMDSGIFLDNRYKMDYPEMGLCIVINNKNFHKSTGMAPRLGTDVDAASIRETFMNLKYEVRNKND
          .HGSKS..SGIFLDN...M.Y.EMGLC.VIN.KNFH.STGM.....TDVDAA.IRE...N..YE.RNKND
Retrocopy LHGSKSVNSGIFLDNGFEMSYSEMGLCTVINKKNFH*STGMTAWSDTDVDAANIREILINFNYELRNKND

Parental  LSCEEIMNLMYSVSKEDHSKRSSFVCVILSHGEE
          L.CE.IM.L.....KEDHSK.SS.VC..LSH..E
Retrocopy LTCEKIMELISKIPKEDHSKTSSIVCIMLSHRQE

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	0.00 RPM	1.38 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1203 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1203 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,