RetrogeneDB ID: retro_cpor_180

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:51448578..51448888(+)
• Located in intron of: ENSCPOG00000014936

Retrocopy information

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

Parental gene information

• Parental gene symbol: AIF1
• Ensembl ID: ENSCPOG00000002068
• Aliases: None
• Description: None

Sequence

>retro_cpor_180
GCTATGAGCCCAAACAAGGATTCACAGAGAGGAAAAGCTTTCGGACTGCTGAAGGCACAGCAAGAAGGGAGATTGGAGGA
GATCAACAAGCAATTCCTGGATGATCCCAAATACAACCGTGATGAGGACCTGCCCTCCAAACTGGAAGCCTTCAAGAAGA
AATACATGGATTTGACCTGAATGGAAATGGAGACAATGATGTCATGTTCTTGAAGAGAATGCTACTGAAACTTAGGGCCC
TCAAGACCCACTCAAGCTAAAGAAATTAACTGGAGAGGCATCTGGTGGCTCAGCTGCCCTGACTTTCTCA

Alignment

ORF - retro_cpor_180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.42 %
• Parental protein coverage: 69.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AMSQTRDFQGGKAFGLLKAQQEERLEEINKQFLDDPKYSTDEDLPSKLEAYKKKYME-FDLNGNGDIDIM
          AMS...D.Q.GKAFGLLKAQQE.RLEEINKQFLDDPKY..DEDLPSKLEA.KKKYM..FDLNGNGD.D.M
Retrocopy AMSPNKDSQRGKAFGLLKAQQEGRLEEINKQFLDDPKYNRDEDLPSKLEAFKKKYMD<FDLNGNGDNDVM

Parental  SLKRMLEKLGVPKTH-LELKKLIGEVSGGSGE-TFS
          .LKRML.KL...KTH.L.LKKL.GE.SGGS...TFS
Retrocopy FLKRMLLKLRALKTH<LKLKKLTGEASGGSAALTFS

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	7.53 RPM
SRP017611_kidney	0.00 RPM	18.42 RPM
SRP017611_liver	0.00 RPM	21.46 RPM
SRP040447_lung	0.00 RPM	24.94 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.87 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_180 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_180 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000002068	2 retrocopies	retro_cpor_180 , retro_cpor_532,