RetrogeneDB ID: retro_cpor_355

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_13:40434978..40435418(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLE3
• Ensembl ID: ENSCPOG00000000313
• Aliases: None
• Description: None

Sequence

>retro_cpor_355
ATGGCGGTGAGGCCCGAGGACCTAAACCTGCCCAATGCTGTCATCACCAGGACCCTCAGAGAAGCACTCCTGGATAGTGT
CAGCATCTCCAAGCAGGCCTGGAGCCCCAGGTCCCATGCAGCCAACATCTTTGTGCTATAGGTCACATCCTGTGCCAACA
ACTTTACAAGGAAAGGGAAACGCAAGACACTCAGTGCCAGTGATGTGCTCTCAGCCATGAAGAGGTGGAAATCCAGAGAT
GTATTACCCCAGTGAAAGAAGCTCTGGAAGCATATAGGCGAGAGCAGAAAGGCGAGAAGGAAGCTTCAGAACAAAAGAAG
AGAGTCAAAGACAGCAAAAAAGATTTGGAAGAGCAAGGCAGAAGCAGGGATGATGATAACGGTGCAGATGAAGAAAGGCT
GGAAGAAGAAGAACAGAATGAGGAGGAGGAAGCAGACAAC

Alignment

ORF - retro_cpor_355 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAERPEDLNLPNAVITRIIKEALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVL
          MA.RPEDLNLPNAVITR...EAL.D.V.ISK.A.S..S.AA..FVL..TSCANNF..KGKRKTL.ASDVL
Retrocopy MAVRPEDLNLPNAVITRTLREALLDSVSISKQAWSPRSHAANIFVL*VTSCANNFTRKGKRKTLSASDVL

Parental  SAM-EEMEFQRFITPLKEALEAYRREQKGKKEASEQKKRDKDKKTDSEEQDRSRDEDNDEDEEKLEEEEQ
          SAM.EE.E.QR.ITP.KEALEAYRREQKG.KEASEQKKR.KD.K.D.EEQ.RSRD.DN..DEE.LEEEEQ
Retrocopy SAM<EEVEIQRCITPVKEALEAYRREQKGEKEASEQKKRVKDSKKDLEEQGRSRDDDNGADEERLEEEEQ

Parental  NEEEEVDN
          NEEEE.DN
Retrocopy NEEEEADN

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	0.23 RPM	18.75 RPM
SRP017611_kidney	0.10 RPM	12.98 RPM
SRP017611_liver	0.00 RPM	9.84 RPM
SRP040447_lung	0.00 RPM	13.14 RPM
SRP040447_skeletal_muscle	0.00 RPM	8.57 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_355 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_355 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017917	1 retrocopy	retro_cjac_4121,
Cavia porcellus	ENSCPOG00000000313	1 retrocopy	retro_cpor_355 ,
Cavia porcellus	ENSCPOG00000003213	1 retrocopy	retro_cpor_901,
Dipodomys ordii	ENSDORG00000003073	2 retrocopies	retro_dord_526, retro_dord_652,
Monodelphis domestica	ENSMODG00000004358	3 retrocopies	retro_mdom_1680, retro_mdom_1920, retro_mdom_647,
Mus musculus	ENSMUSG00000028394	2 retrocopies	retro_mmus_124, retro_mmus_555,
Pteropus vampyrus	ENSPVAG00000004717	1 retrocopy	retro_pvam_302,
Rattus norvegicus	ENSRNOG00000015392	1 retrocopy	retro_rnor_55,
Ictidomys tridecemlineatus	ENSSTOG00000027365	1 retrocopy	retro_itri_866,
Tupaia belangeri	ENSTBEG00000005211	1 retrocopy	retro_tbel_4052,