RetrogeneDB ID: retro_cpor_439

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_155:1971570..1971885(+)
• Located in intron of: ENSCPOG00000003790

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSMP
• Ensembl ID: ENSCPOG00000021717
• Aliases: None
• Description: None

Sequence

>retro_cpor_439
CCAGGAGCCCACAGCAAGTGCTGCTTCCAAGCTCGAGCTCCCTGTGGGAGGAGAGGACAGAGTTCACCCTGGGGAGTCTG
AGCTCCGATAGGACTTCTCTGCTGCCCATCTTCGTCCTGTCAGCGCTGGCTGCCTGGTGTGGCTCAGCATCCCCATCGAC
TCCCCGCTGGGTGAGGCTGGGGGGGAGGCTGGAGCCTGCCAGTTTTCCTTGGTGCAAAAATCTGATCCTTGGTGGCCCTG
CAGAGGTGGAGGGCCGACCTCGAGTGGGGCTCAGCTAACACCCCTATTCCCGGGGCTTCTGCTCCCCACCCCAGC

Alignment

ORF - retro_cpor_439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.36 %
• Parental protein coverage: 77.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PGVHTKCYFQAQAPCHYEGKY-FTLG-ESWLREDCFHCTCLHPVGVGCCDTSQHPIDFPAECEVRREAGT
          PG.H.KC.FQA.APC...G...FTLG.ES.LR.D.F....L.PV..GC......PID.P...E...EAG.
Retrocopy PGAHSKCCFQARAPCGRRGQS<FTLG<ESELR*D-FSAAHLRPVSAGCLVWLSIPIDSPLG-EAGGEAGA

Parental  CQFSLVQKSDPRLPCKSRGP-DLEWGSANTPVPGAPAPHSS
          CQFSLVQKSDP..PC...GP.DLEWGSANTP.PGA.APH.S
Retrocopy CQFSLVQKSDPWWPCRGGGP<DLEWGSANTPIPGASAPHPS

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	12.31 RPM
SRP017611_kidney	0.00 RPM	11.41 RPM
SRP017611_liver	0.13 RPM	6.44 RPM
SRP040447_lung	0.00 RPM	12.96 RPM
SRP040447_skeletal_muscle	0.00 RPM	4.14 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_439 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_439 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	ENSCPOG00000021717	1 retrocopy	retro_cpor_439 ,