RetrogeneDB ID: retro_cpor_725

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_25:1670165..1670908(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPKOW
• Ensembl ID: ENSCPOG00000013270
• Aliases: None
• Description: None

Sequence

>retro_cpor_725
GTACTGTCCCAGACTGTGATGCAGTTCTATGAGGAATCCAAGATGTCTCTAGAGGAAGGAAATAATGCAAGTGTTGATCC
CAGGCACACTATCTTCATGATTCAGAAAGGATGCATACCTCAATGGAAAAAAAGTGAACAGTGAGCCCTGGCTGAGCCAG
AGCCAGAGGTTGATTATGAGGCAGTCCCTGTGGAACCCTATGGGTTGGCCATGATGCAGGGCATGGGCTGGAAACCTGGA
AAGATCATTGGCTGAACTTTTCAATCAAGTGGGCAAGCCCAGTGTAAACTCTAAAGCCCCCAAGGGGTTAGGAATGGGTG
CCAACCTGACCAAAGCCCAGGCATTTGCTTTCATTGCCTGCTGCTTCCTACCAAAGCCAGATGGGGAGCAAGAGAATGAT
AAGGAAGACCAAACTGAAGGGGCTGCTGCCTGGAGGCACTGTGGTGGTTCTTTCTGGCCCTCATCAACACCTCTATTGGA
AGCGAGAAGGCCTTGATCCTGACAATGTACAGGTCGTGGATCATCTAGCAATGGGCTATCACATACCAACTGTTAGCAAC
CTGTGACCTGTACCCCAGCAGAAGTTTGACAAGAATTTCTTGCACCCAGTCCAGGTCCAGATGAGCAGAACTTGCTCTCT
ACAACACATTGGAACAGCTTTATTATGGAAGGCACTCCAAAGTGAAAACTTGCATGGCCAGCAGGAGAACACAGAGAGGA
AATGGAAACACCCTCTAGATAAG

Alignment

ORF - retro_cpor_725 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.94 %
• Parental protein coverage: 51.98 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLSQAVKELIEESKKSLEERENAGVDPSLAIPMIQKGCIPGEEGADSTPRAETVPEEADYEAVPVEAYGL
          VLSQ.V....EESK.SLEE..NA.VDP...I.MIQKGCIP..........AE..PE..DYEAVPVE.YGL
Retrocopy VLSQTVMQFYEESKMSLEEGNNASVDPRHTIFMIQKGCIPQWKKSEQ*ALAEPEPE-VDYEAVPVEPYGL

Parental  AMLRGMGWKPGEGIGRTF-NQVVKPRVNLLRPKGLGLGASLTEAQALPSSGSYCPPKPGGEQKKGKEDQP
          AM..GMGWKPG..IG.TF.NQV.KP.VN...PKGLG.GA.LT.AQA.........PKP.GEQ...KEDQ.
Retrocopy AMMQGMGWKPGKIIG*TF>NQVGKPSVNSKAPKGLGMGANLTKAQAFAFIACCFLPKPDGEQENDKEDQT

Parental  QG-LVPGRTVVVLSGPHRGLYGKVEGLDPDNVRAMVRLALGSRMVTVSEYCLRPVSQQEFDKNLHSDKIG
          .G.L.PG.TVVVLSGPH..LY.K.EGLDPDNV.....LA.G....TVS...L.PV.QQ.FDKN.......
Retrocopy EG>LLPGGTVVVLSGPHQHLYWKREGLDPDNVQVVDHLAMGYHIPTVSN--L*PVPQQKFDKNFLHPVQV

Parental  QASRTSLGQHNGSSLSRKAHQSEDLRGRQEDPEKKRKHPPDR
          Q.SRT...QH.G..L..KA.QSE.L.G.QE..E.K.KHP.D.
Retrocopy QMSRTCSLQHIGTALLWKALQSENLHGQQENTERKWKHPLDK

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	29.97 RPM
SRP017611_kidney	0.00 RPM	25.02 RPM
SRP017611_liver	0.00 RPM	17.89 RPM
SRP040447_lung	0.00 RPM	30.29 RPM
SRP040447_skeletal_muscle	0.00 RPM	12.46 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_725 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_725 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013270	2 retrocopies	retro_cpor_148, retro_cpor_725 ,
Felis catus	ENSFCAG00000003818	1 retrocopy	retro_fcat_1267,
Mus musculus	ENSMUSG00000031148	1 retrocopy	retro_mmus_3156,