RetrogeneDB ID: retro_cpor_1091

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_45:4932177..4932339(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ELOF1
• Ensembl ID: ENSCPOG00000020359
• Aliases: None
• Description: None

Sequence

>retro_cpor_1091
TTCTGTTCCACAACAAGCCTTGCTGTTAAAATGAACCATGCCTGCAATACTGAAGTAATGTCTTATGCCCTGTGCCTACA
GAAATTCCAGATATCTATGACATATCTGTCAGAAACAGTATATTTGTACATAAGATGGATAGTTGCCTATGAGGTGGCCA
AT

Alignment

ORF - retro_cpor_1091 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.91 %
• Parental protein coverage: 66.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDACEAAN
          FC....S..VKM..A.NT.V.S...CL..FQ...TYLSE.V..Y..WI.A.E.AN
Retrocopy FCS-TTSLAVKMNHACNTEVMSYALCLQKFQISMTYLSETVYLYIRWIVAYEVAN

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	12.54 RPM
SRP017611_kidney	0.00 RPM	13.50 RPM
SRP017611_liver	0.00 RPM	7.97 RPM
SRP040447_lung	0.00 RPM	9.51 RPM
SRP040447_skeletal_muscle	0.00 RPM	6.63 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1091 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1091 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000064	1 retrocopy	retro_amel_1495,
Cavia porcellus	ENSCPOG00000020359	1 retrocopy	retro_cpor_1091 ,
Felis catus	ENSFCAG00000004926	1 retrocopy	retro_fcat_699,
Loxodonta africana	ENSLAFG00000001534	2 retrocopies	retro_lafr_1217, retro_lafr_771,
Macropus eugenii	ENSMEUG00000012101	1 retrocopy	retro_meug_2078,
Otolemur garnettii	ENSOGAG00000026211	1 retrocopy	retro_ogar_2878,
Ictidomys tridecemlineatus	ENSSTOG00000003687	1 retrocopy	retro_itri_1081,
Tupaia belangeri	ENSTBEG00000004812	1 retrocopy	retro_tbel_2163,
Tursiops truncatus	ENSTTRG00000001807	1 retrocopy	retro_ttru_1611,