RetrogeneDB ID: retro_cpor_306

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_12:35443802..35445033(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PELI1
• Ensembl ID: ENSCPOG00000009443
• Aliases: None
• Description: None

Sequence

>retro_cpor_306
ATGTTTTATCCTGATCAAGAAAATCATCCTTTGGAAGCATGAGTAAAATATGGTGAACTCATTGTGTTAGGGTGTAATGA
GTTTCTCCCAAATGGCGATAGAGGAAGAAGAAAAAGTAGGTTTGCTTTGCTTAAAACGCCTAAGGCAAATGGGGTGAAGC
CTGGCACACTGTGTATTCCTCAGGCTGCAAAGGCAGTAAGCAGTGAGGACCTGTATAGCACATCATGTATCTTACCTCGG
ATCCAGTGAGAGGTGGTTGAATATACTCAGGACAGCACCGGCGATATGTTGCAGATTGGTCGGTGGACTGAAAGTTCTAA
TTTTGTGGTAGCTCACACAGTTCCTGGAAGTCAAAGCAATTCTGGTACAGAGACTACGGAAAACACATCAATAGTCACCT
GTTGTGTCATATGTGAATGGAATCTTGTTTTTACAGCAGGGATTTATGCTGCAGGATTTGATTCATCAAACAATATCTTC
GCGGGGAAAGGACTCCAAATGGAAGACGTCTGATGGGCACATGGATGCCTTAATCACTAAAGGTGTTCTTGTGATGCATC
CACACAATGGGTTCACAGAAGACTAAGCCCAGAAGATGAAGAGAAATATCAGCGTGTGGAAATGTATTTGGCCTGCGTGA
GGCCAGAGGAGCTCAGTAAAAGAGGAAAACCAGTGGGAATTGAAACCAATCAGTTACTAGATGGCTCATTAATTGATCTC
TGAGGTGCAACATTGCTGCACCTCAGAATTGTGGAAGGCCTTTTCCATGCTTCTACTGTGAGGCATTTAGAAACTTTAAG
ACAGTAAATTAATGCAGCAAGACCTCAGTGCCCTGCAGGGTACAACACAACAACATTTCACAATATGACAAAGAAAGATG
TAGATGAGAAACAACCGCAGGCATATTGAAACTGTGGCCGTGTACATAGCTATCATAACTGGGGAACTGAAGAATTTGAT
GGAAAAGATCATAAATGTGCTGTGTATAGATCTGTTGGTCCCTGTGTCCCTCTGTGGCTTGGATGTGAAGCTAGATTTTA
CGTGAATGCTGACCCTCCAACCCATGCCTTTGGCCCTTGTGGTCACGTGTGTTGAGAGAAGACGGTTGCCTATTGCCCCC
AGACCCAGCTTCCTCATGGAATGCATCCTTTTCAGCAGTCTGTCCTTTCTGTTCAGTGAGTTAACTAGTGAACAAGGCAA
CATCAGACTTATTTTCCAAGAACCAGTAGAC

Alignment

ORF - retro_cpor_306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 8
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MFSPDQENHPSKAPVKYGELIVLGYNGSLPNGDRGRRKSRFALFKRPKANGVKPSTVHIACTPQAAKAIS
          MF.PDQENHP..A.VKYGELIVLG.N..LPNGDRGRRKSRFAL.K.PKANGVKP.T....C.PQAAKA.S
Retrocopy MFYPDQENHPLEA*VKYGELIVLGCNEFLPNGDRGRRKSRFALLKTPKANGVKPGTL---CIPQAAKAVS

Parental  NKDQHSISYTLSRAQTVVVEYTHDSNTDMFQIGRSTESPIDFVVTDTVPGSQSNSDTQSVQSTISRFACR
          ..D..S.S..L.R.Q..VVEYT.DS..DM.QIGR.TES...FVV..TVPGSQSNS.T.....T.S...C.
Retrocopy SEDLYSTSCILPRIQ*EVVEYTQDSTGDMLQIGRWTESS-NFVVAHTVPGSQSNSGTETTENT-SIVTCC

Parental  IICERNPPFTARIYAAGFDSSKNIFL-GE-KAAKWKTPDGQMDGLTTNGVLVMHPRNGFTEDSKPGIWRE
          .ICE.N..FTA.IYAAGFDSS.NIF..GE.K..KWKT.DG.MD.L.T.GVLVMHP.NGFTED......R.
Retrocopy VICEWNLVFTAGIYAAGFDSSNNIFA<GE<KDSKWKTSDGHMDALITKGVLVMHPHNGFTED*AQKMKRN

Parental  ISVCGNVFSLRETRSA-QQRGKMVEIETNQLQDGSLIDLCGATLL-WRTAEGLSHTPTVKHLEALRQEIN
          ISV..........RS....RGK.V.IETNQL.DGSLIDL.GATLL..R..EGL.H..TV.HLE.LRQ.IN
Retrocopy ISVWKCIWPA*GQRSS<SKRGKPVGIETNQLLDGSLIDL*GATLLHLRIVEGLFHASTVRHLETLRQ*IN

Parental  AARPQCPVGFNTLAFPSMKRKDVVDEKQPWVYLNCGHVHGYHNWGNKEECDGKDRECPMCRSVGPYVPLW
          AARPQCP.G.NT..F..M..KD.VDEKQP..Y.NCG.VH.YHNWG..EE.DGKD..C...RSVGP.VPLW
Retrocopy AARPQCPAGYNTTTFHNMTKKD-VDEKQPQAY*NCGRVHSYHNWGT-EEFDGKDHKCAVYRSVGPCVPLW

Parental  LGCEAGFYVDAGPPTHAFSPCGHVCSEKTTAYWSQIPLPHGTH-TFHAACPFCA-HQLAGEQGYIRLIFQ
          LGCEA.FYV.A.PPTHAF.PCGHVC.EKT.AY..Q..LPHG.H..F.A.CPFC....L..EQG.IRLIFQ
Retrocopy LGCEARFYVNADPPTHAFGPCGHVC*EKTVAYCPQTQLPHGMH<SFSAVCPFCS<SELTSEQGNIRLIFQ

Parental  GPLD
          .P.D
Retrocopy EPVD

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	14.61 RPM
SRP017611_kidney	0.00 RPM	6.28 RPM
SRP017611_liver	0.00 RPM	7.97 RPM
SRP040447_lung	0.00 RPM	28.58 RPM
SRP040447_skeletal_muscle	0.00 RPM	6.77 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_306 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_306 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	ENSCPOG00000009443	1 retrocopy	retro_cpor_306 ,
Rattus norvegicus	ENSRNOG00000006329	1 retrocopy	retro_rnor_586,