RetrogeneDB ID: retro_cpor_1198

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_55:7037894..7038253(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARFRP1
• Ensembl ID: ENSCPOG00000014423
• Aliases: None
• Description: None

Sequence

>retro_cpor_1198
GGTGTAAACACTGCCACCGTGGAAGTAGGAAAGGCTTGCCTCATGTTCTGGGACTTAGGACTGGAAGAGCTGCAGTCTTT
GTGGGACAAGTACCGTGCAGAGTGCCATGTCGTCTTCTGTGTCACGGACTCCACTGATGAAAGGAGACTGTCAGAATCCA
AGCAGGCATTCAAGAAGGTGGTTTGGAGTGAGTATCTTGACAACGCCCTATCCTGGTGCTGGCTAACAAACCGGATGTGG
AGAAGTGCCTCTTGATCCCTGACATCAAGACCGCATTTAGTGACTGCACCTGTAAGATCAGCACGCGAGACTGTCTGACC
CAGGCCTGCTCTGCCCACATAGGCAAAGGAATACAAGAG

Alignment

ORF - retro_cpor_1198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.05 %
• Parental protein coverage: 60.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GLNIGTVDVGKARLMFWDLGGQEELQSLWDKYYAECHGVIYVIDSTDEERLSESKQAFEKVVSSESLDGV
          G.N..TV.VGKA.LMFWDLG..EELQSLWDKY.AECH.V..V.DSTDE.RLSESKQAF.KVV.SE.LD..
Retrocopy GVNTATVEVGKACLMFWDLG-LEELQSLWDKYRAECHVVFCVTDSTDERRLSESKQAFKKVVWSEYLDNA

Parental  -PILVLANKQDVETCLSIPDIKTAFSDCTCKIGRRDCLTQACSALTGKGVRE
          .PILVLANK.DVE.CL.IPDIKTAFSDCTCKI..RDCLTQACSA..GKG..E
Retrocopy <PILVLANKPDVEKCLLIPDIKTAFSDCTCKISTRDCLTQACSAHIGKGIQE

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	20.48 RPM
SRP017611_kidney	0.00 RPM	25.44 RPM
SRP017611_liver	0.00 RPM	10.97 RPM
SRP040447_lung	0.03 RPM	36.55 RPM
SRP040447_skeletal_muscle	0.00 RPM	24.35 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1198 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1198 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014423	1 retrocopy	retro_cpor_1198 ,
Erinaceus europaeus	ENSEEUG00000005894	1 retrocopy	retro_eeur_378,