RetrogeneDB ID: retro_cpor_916

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_33:13946010..13946219(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTMA
• Ensembl ID: ENSCPOG00000022634
• Aliases: None
• Description: None

Sequence

>retro_cpor_916
AACCCAGAGAAGGGCAAGCGGGAGGCTGACCTGCAGGTAGACGAAGAGTAAGAGGAAGGTGGGCATGCAGAGGAAAATGT
GATGGTAAAGAAGAGAATGGAGATGGAGATGAAGAGGCAAAGGCAACTACCAGCAGACAGATAGCTGAAGATGATCAAGA
TGAGGGTGATGGCTTGGACACCAAGAAGCAGAACACAGATGAGGGTGAC

Alignment

ORF - retro_cpor_916 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.7 %
• Parental protein coverage: 77.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NEENGEQEADNEVDEEEEEGGEEEEEEE-EGEGEEEDGDEDEEAEAATGKRAAEDDED--DDVDTKKQKT
          N.E.G..EAD..VD...EE..E....EE....G.EE.GD.DEEA.A.T....AEDD.D..D..DTKKQ.T
Retrocopy NPEKGKREADLQVD---EE*EEGGHAEE<KCDGKEENGDGDEEAKATTSRQIAEDDQDEGDGLDTKKQNT

Parental  DEDD
          DE.D
Retrocopy DEGD

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	41.76 RPM
SRP017611_kidney	0.00 RPM	102.49 RPM
SRP017611_liver	0.00 RPM	40.39 RPM
SRP040447_lung	0.00 RPM	144.54 RPM
SRP040447_skeletal_muscle	0.00 RPM	26.63 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_916 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_916 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016287	1 retrocopy	retro_amel_1811,
Choloepus hoffmanni	ENSCHOG00000006234	1 retrocopy	retro_chof_60,
Cavia porcellus	ENSCPOG00000022634	1 retrocopy	retro_cpor_916 ,