RetrogeneDB ID: retro_cpor_148

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_0:20866058..20866992(-)
• 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_148
CAGGCAGTCCCTATAGAGGCCTTTGGGCTAGCCATGCTTCAGGGTATGGGCTGGCAACCTGGTGAAGGCATTTGTCATAC
TTTCAATCAAGTGCTAAAGCCTTGTGTAAAGTCACTGAGGCCCAAGGGGTTAAGGCTGTGTGCCAACCTGACAAGGCCCA
GGCCTTGGCCTCCAGTGGTTTCTACCACCCACCAAAGCCAGACAGGGAGCAAGAGAAGGATAAGGAAAATCAAACTCAAG
GGCTGTTGAAGGCACTATGGTGGTCCTTTCTGACCCTTATCAGCACCTCTATGGAAAGGTGGAAGGCCTTGATCCTGATA
ATGTGTGGGCCGTGGTTCAGCTAGCAGTAGGCAGTCACATCATGACTATTAGCAGCTACTGCCTGCAACCTGTGTCCCAG
CAGGAATTTCACAAGAATTTCTTGCATCCTGTCCAGCTGAGCAGAACATGCTTTGGACAACACAATGGAATAGCCTGTTA
CAGAAGGCCCTCGAGAATAAAGACCTGCATGACCCTTGAAGGACTTAGACAGAAAGTGGAAATACCCCGCGGACCTACGG
GATGGGCCTGCAGCCAAGAGAGAGAAAGCAGCCAGCAGGAGTCAGCAGTAGCTGCACAGGGACCTGCGCGTGCACTTCGT
GGACAAGTGGCAAAAGTGCGGCCACTATTACAACACTAAGATGACGATTGAAGACGTTCTGAGTCCAGATACCTGTACGT
GCAGGACAGATGAAGACTGAGTCCTGGAAGGTGTGAGGGAAGACATGCTGGAGACCCTGGTTCCCAAGGGCGAGGGTGAT
TGGGTGACGGTGGTGCGGTGGCCACAGGCTGGGAGAGTGGACATCTGCGGGGCAGGGACAGAGTGTGGAGCCAGGCTTTG
GTGCAACCGTGGACAGAGAATCACCTGGTGGAGTTTTACTACAATGCCGTGTGT

Alignment

ORF - retro_cpor_148 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.46 %
• Parental protein coverage: 65.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EAVPVEAYGLAMLRGMGWKPGEGIGRTFNQVVKPRVNLLRPKGLGLGASLT-EAQALPSSGSYCPPKPGG
          .AVP.EA.GLAML.GMGW.PGEGI..TFNQV.KP.V..LRPKGL.L.A.LT..AQAL.SSG.Y.PPKP..
Retrocopy QAVPIEAFGLAMLQGMGWQPGEGICHTFNQVLKPCVKSLRPKGLRLCANLT<KAQALASSGFYHPPKPDR

Parental  EQKKGKEDQPQGL-VPGRTVVVLSGPHRGLYGKVEGLDPDNVRAMVRLALGSRMVTVSEYCLRPVSQQEF
          EQ.K.KE.Q.QGL.V.G.T.VVLS.P...LYGKVEGLDPDNV.A.V.LA.GS...T.S.YCL.PVSQQEF
Retrocopy EQEKDKENQTQGL<VEG-TMVVLSDPYQHLYGKVEGLDPDNVWAVVQLAVGSHIMTISSYCLQPVSQQEF

Parental  DKN-LHSDKIGQASRTSLGQHNG-SSLSRKAHQSEDLRG-RQEDPEKKRKHPPDRQDGPVAKSEKAASRS
          .KN.LH.......SRT..GQHNG..SL..KA....DL......D...K.K.P.D..DGP.AK.EKAASRS
Retrocopy HKNFLHPVQL---SRTCFGQHNG<NSLLQKALENKDLHD<PLKDLDRKWKYPADLRDGPAAKREKAASRS

Parental  QHWLHRDLRVRFVDKLYKGGQYYNTKMTIEDVLSPDTCVCRTDKGQVLEGLREDMLETLVPKVEGDRVMV
          Q..LHRDLRV.FVDK..K.G.YYNTKMTIEDVLSPDTC.CRTD...VLEG.REDMLETLVPK.EGD.V.V
Retrocopy QQ*LHRDLRVHFVDKWQKCGHYYNTKMTIEDVLSPDTCTCRTDED*VLEGVREDMLETLVPKGEGDWVTV

Parental  VLGPQAGRV-GHLLGRDRAHNRALVQLQRENQLVELHYDAVC
          V..PQAGRV.GHL.GRDR....ALVQ...EN.LVE..Y.AVC
Retrocopy VRWPQAGRV<GHLRGRDRVWSQALVQPWTENHLVEFYYNAVC

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	0.10 RPM	25.02 RPM
SRP017611_liver	0.04 RPM	17.89 RPM
SRP040447_lung	0.20 RPM	30.29 RPM
SRP040447_skeletal_muscle	0.01 RPM	12.46 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_148 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_148 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,