RetrogeneDB ID: retro_cpor_1117

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_47:13355202..13355553(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYB5B
• Ensembl ID: ENSCPOG00000014234
• Aliases: None
• Description: None

Sequence

>retro_cpor_1117
ATGGTGACTGTGGAGGGTGGCAGCAGTGGCAAGAAAGGGCAGGACAGCAAGACCTCTGCCACTTACTATTGGTTGGAGGA
GGTGGTGAAGCACAACTCTTAGAAGGAACTGTGGCTGGTGACCCACTGGTGAGTCTACGGTGCCACTCCCTTTCTTAATG
AGCGTCCTGGTGGAGAAGATGTTCTGCTGGAACAGGCTGGTGTAGATGCAAGTGAAAGCTTTGCAGATGGAGGCCATTCC
TCTAATGCCAGAAAGATGCTAAAGCAGTACTACATTGGTGATTTCCATCCGAATGACCTTAAACCTCAAAGCAGTAACAA
GGATCCTTCGAAAAAGTCGTGCAAAAGTTGT

Alignment

ORF - retro_cpor_1117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.42 %
• Parental protein coverage: 80.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATVEGGSSGEKGQGGETTVTYYRLEEVAKHNSLKELWLVIHGRVYDVTPFLNEHPGGEEVLLEQAGIDA
          M.TVEGGSSG.KGQ...T..TYY.LEEV.KHNS.KELWLV.H..VY..TPFLNE.PGGE.VLLEQAG.DA
Retrocopy MVTVEGGSSGKKGQDSKTSATYYWLEEVVKHNS*KELWLVTHW*VYGATPFLNERPGGEDVLLEQAGVDA

Parental  SESFEDVGHSSDAREMLKQYYIGDLHPSDLKPQSGSKGPSKNNSCKSC
          SESF.D.GHSS.AR.MLKQYYIGD.HP.DLKPQS..K.PSK..SCKSC
Retrocopy SESFADGGHSSNARKMLKQYYIGDFHPNDLKPQSSNKDPSK-KSCKSC

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	13.69 RPM
SRP017611_kidney	0.00 RPM	14.55 RPM
SRP017611_liver	0.00 RPM	39.17 RPM
SRP040447_lung	0.00 RPM	23.96 RPM
SRP040447_skeletal_muscle	0.00 RPM	4.03 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1117 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1117 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 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000007518	1 retrocopy	retro_apla_13,
Cavia porcellus	ENSCPOG00000012111	1 retrocopy	retro_cpor_1140,
Cavia porcellus	ENSCPOG00000014234	1 retrocopy	retro_cpor_1117 ,
Felis catus	ENSFCAG00000024541	1 retrocopy	retro_fcat_1816,
Gallus gallus	ENSGALG00000000660	1 retrocopy	retro_ggal_13,
Meleagris gallopavo	ENSMGAG00000008619	1 retrocopy	retro_mgal_12,
Myotis lucifugus	ENSMLUG00000006608	1 retrocopy	retro_mluc_1734,
Macaca mulatta	ENSMMUG00000012039	1 retrocopy	retro_mmul_128,
Mus musculus	ENSMUSG00000031924	1 retrocopy	retro_mmus_2289,
Oryctolagus cuniculus	ENSOCUG00000007729	2 retrocopies	retro_ocun_141, retro_ocun_255,
Pteropus vampyrus	ENSPVAG00000015984	1 retrocopy	retro_pvam_977,
Sarcophilus harrisii	ENSSHAG00000014200	1 retrocopy	retro_shar_688,
Ictidomys tridecemlineatus	ENSSTOG00000011316	1 retrocopy	retro_itri_1296,
Tursiops truncatus	ENSTTRG00000010016	1 retrocopy	retro_ttru_521,
Drosophila melanogaster	FBgn0029854	1 retrocopy	retro_dmel_39,