RetrogeneDB ID: retro_cpor_1102

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_46:1164483..1164660(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLE4
• Ensembl ID: ENSCPOG00000027003
• Aliases: None
• Description: None

Sequence

>retro_cpor_1102
AAACTCCAACCTGATGTTCAGGGGACAGGAATTCATATTTGTTCTGACACAAGTTGACTATGTGTGGAGATCATTGCAAA
AGATGCCTGCTGCAGTGTTCACCAAGGAAGGAAAAAAACTCTCCAGGGGATAGATTTGGATGATGCCATCGAACTGGATG
AAGTTACTTTTCTGGAA

Alignment

ORF - retro_cpor_1102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.79 %
• Parental protein coverage: 56.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KADPDVTLAGQEAIFVLARAAELFVETIAKDAYCCAQQGKRKTLQRRDLDNAIEAVDEFAFLE
          K..PDV...G...I........L.VE.IAKDA.C...QG..KTLQ..DLD.AIE..DE..FLE
Retrocopy KLQPDVQGTG---IHICSDTS*LCVEIIAKDACCSVHQGRKKTLQGIDLDDAIE-LDEVTFLE

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	4.83 RPM
SRP017611_kidney	0.00 RPM	16.02 RPM
SRP017611_liver	0.00 RPM	5.75 RPM
SRP040447_lung	0.00 RPM	7.82 RPM
SRP040447_skeletal_muscle	0.00 RPM	2.67 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1102 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1102 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017073	1 retrocopy	retro_amel_394,
Callithrix jacchus	ENSCJAG00000017156	1 retrocopy	retro_cjac_1087,
Cavia porcellus	ENSCPOG00000027003	1 retrocopy	retro_cpor_1102 ,
Felis catus	ENSFCAG00000005983	1 retrocopy	retro_fcat_790,
Homo sapiens	ENSG00000115350	1 retrocopy	retro_hsap_2765,
Gorilla gorilla	ENSGGOG00000004491	1 retrocopy	retro_ggor_1924,
Mustela putorius furo	ENSMPUG00000008356	1 retrocopy	retro_mputfur_305,
Nomascus leucogenys	ENSNLEG00000001111	1 retrocopy	retro_nleu_670,
Pongo abelii	ENSPPYG00000012258	1 retrocopy	retro_pabe_2246,
Pan troglodytes	ENSPTRG00000012105	1 retrocopy	retro_ptro_1872,