RetrogeneDB ID: retro_cpor_373

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_136:290136..290488(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL5
• Ensembl ID: ENSCPOG00000003343
• Aliases: None
• Description: None

Sequence

>retro_cpor_373
AAAATACTTAGTAAGGAAGAGGAAGAGTTTGAGTTAACAAATGTTGGCATGATTCAGTGTACTATATGCTCATTAGCTAC
CAGAATATTCAAGTAATTTGATACAGTAATTATAAAACTCCCTTTTGGTACCAAAACTAATTAAAGGGACAGGGATGGCT
TCATTGGAGAATACATTGAAAATGGCAAGAATATTAACAAAATTCTTAAGGAGAGTACAGATTCAAAACAAAGCCACAAA
ATGAAAAGTCAAGATATACATTTGTACAGAAATTTGATGCCTTTCAGCATCACATAAATTTTATAAAAAGAAATTAGTAG
ACACTGAAGTGGACTTAATTTGATTTTCTTTT

Alignment

ORF - retro_cpor_373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.22 %
• Parental protein coverage: 58.94 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EIFNRNVEEFELTNVDMVQCDVCSLSNRMAKSFDTVIMNPPFGTKNN-KGIDMTFLKTALEMARTAVYSL
          .I.....EEFELTNV.M.QC..CSL..R..K.FDTVI...PFGTK.N.KG..M..L...L.MAR.....L
Retrocopy KILSKEEEEFELTNVGMIQCTICSLATRIFK*FDTVIIKLPFGTKTN>KGTGMASLENTLKMARI----L

Parental  HKSSTREHVQKKAAEWKIKIDIIAELRYDLPALYNFHKKKSVDIEVDLIRFSF
          .K...R...Q.KA...K.KI.I..E....L.A...F.KKK.VD.EVDLI.FSF
Retrocopy TKFLRRVQIQNKATK*KVKIYICTEI*C-LSASHKFYKKKLVDTEVDLI*FSF

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	9.55 RPM
SRP017611_kidney	0.00 RPM	9.53 RPM
SRP017611_liver	0.00 RPM	10.23 RPM
SRP040447_lung	0.00 RPM	10.24 RPM
SRP040447_skeletal_muscle	0.00 RPM	14.92 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_373 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_373 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003343	1 retrocopy	retro_cpor_373 ,
Dasypus novemcinctus	ENSDNOG00000013460	2 retrocopies	retro_dnov_1043, retro_dnov_773,
Homo sapiens	ENSG00000138382	2 retrocopies	retro_hsap_1365, retro_hsap_2930,
Gorilla gorilla	ENSGGOG00000022484	2 retrocopies	retro_ggor_1064, retro_ggor_2032,
Loxodonta africana	ENSLAFG00000018044	2 retrocopies	retro_lafr_1213, retro_lafr_864,
Macaca mulatta	ENSMMUG00000023054	3 retrocopies	retro_mmul_1430, retro_mmul_1953, retro_mmul_2193,
Nomascus leucogenys	ENSNLEG00000005018	4 retrocopies	retro_nleu_1070, retro_nleu_1919, retro_nleu_753, retro_nleu_990,
Oryctolagus cuniculus	ENSOCUG00000010405	1 retrocopy	retro_ocun_1440,
Pongo abelii	ENSPPYG00000012916	2 retrocopies	retro_pabe_2281, retro_pabe_2523,
Pan troglodytes	ENSPTRG00000012621	3 retrocopies	retro_ptro_1822, retro_ptro_2062, retro_ptro_938,