RetrogeneDB ID: retro_cpor_1218

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_58:3582234..3582526(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C2ORF72
• Ensembl ID: ENSCPOG00000020204
• Aliases: None
• Description: None

Sequence

>retro_cpor_1218
CAAGCCACACTTCCCAGTGTTGGTAGAGGTGGTGGGCAGCTGCAGGCAGAAGGAGCCTGGGAGAGCTGATGGTTCCTGGG
GCTCTGAGCTGGTTCACCTGAGGTCCTGGGGGTCACAGGAAGGAACCAGATGCCACTTCCCAACAGTCAACTCTACAGAC
TCTCAAGGACTCCAAGGATGAGATGACCTCATACCCATCTTTCCCAACAGAGACTGTGAAGACTGTGGCAGCAGATTCAG
AGCTCAGGACAGAGCCACCCACCTTTCCCTGGAGGCCTCTGGAGGCCCAAGA

Alignment

ORF - retro_cpor_1218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.48 %
• Parental protein coverage: 73.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QAAACRLQAAGHGRPAEGAWE-RQQLPGLLSCFAWGPWGHRKERDATFSRGSSQETPQDSEDELA-LTAI
          QA........G....AEGAWE.....PG.LS.F..GP.GHRKE.DAT.S..S...T..DS.DE...L..I
Retrocopy QATLPSVGRGGGQLQAEGAWE<ELMVPGALSWFT*GPGGHRKEPDAT-SQQSTLQTLKDSKDEMT<LIPI

Parental  FPNGDCEDCNIGFRAQDRAARLSPELPGHSR
          FPN.DCEDC...FRAQDRA..LS.E..G..R
Retrocopy FPNRDCEDCGSRFRAQDRATHLSLEASGGPR

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	1.78 RPM
SRP017611_kidney	0.00 RPM	0.10 RPM
SRP017611_liver	0.00 RPM	11.80 RPM
SRP040447_lung	0.00 RPM	0.15 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.00 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1218 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1218 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000020204	1 retrocopy	retro_cpor_1218 ,