RetrogeneDB ID: retro_cpor_504

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_17:37759503..37759853(-)
• Located in intron of: ENSCPOG00000005816

Retrocopy information

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

Parental gene information

• Parental gene symbol: MREG
• Ensembl ID: ENSCPOG00000010037
• Aliases: None
• Description: None

Sequence

>retro_cpor_504
CTGCAGCAGATTCGAAGGGAAGTGAGAAACAGATGGAAACGCATTTTAGAAGATTTAGGTTTTCAAAAGGAAGTGGATTC
TTTGTTGTCAGTGACTAAACTTAGCACCATGAGTGAGTCTAAAAATACGAGGAAAGCCCAAGAGATGTTGTTGAAAGTGG
CTAAGAGACCAGCATTTTTCCAACCAGTTGGGAGCTGTCAGGGAGACACCTATGTGTTGTGGATCGACCCATTCATTGCT
CTTGAGCAGCTGAAGAGTTCTCTAAGATTGCTAGTCAACCTTCGCCCAAGAAGCCTGGGCGATGCCTAGCTGATGACCAG
AGAAAACAACCCTGCCTTCCATTTCCAAGT

Alignment

ORF - retro_cpor_504 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.51 %
• Parental protein coverage: 54.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LRQIRREVRNRWKRILEDLGFQKEVDSLLSVTKLSTMSDSKNTRKAREMLLKLAE-ETSIFPTSWELSER
          L.QIRREVRNRWKRILEDLGFQKEVDSLLSVTKLSTMS.SKNTRKA.EMLLK.A..ETSIFPTSWELS.R
Retrocopy LQQIRREVRNRWKRILEDLGFQKEVDSLLSVTKLSTMSESKNTRKAQEMLLKVAK<ETSIFPTSWELSGR

Parental  YLFVVDRLIALD-AAEEFFKIASQTYPKKPGVPCLANDQKKQPYLPFPS
          .L.VVDR.I....AAEEF.KIASQ..PKKPG..CLA.DQ.KQP.LPFPS
Retrocopy HLCVVDRPIHCS*AAEEFSKIASQPSPKKPG-RCLADDQRKQPCLPFPS

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	5.06 RPM
SRP017611_kidney	0.00 RPM	6.60 RPM
SRP017611_liver	0.00 RPM	0.61 RPM
SRP040447_lung	0.00 RPM	18.89 RPM
SRP040447_skeletal_muscle	0.00 RPM	2.52 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_504 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_504 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	ENSCPOG00000010037	1 retrocopy	retro_cpor_504 ,
Mustela putorius furo	ENSMPUG00000007637	1 retrocopy	retro_mputfur_775,