RetrogeneDB ID: retro_cpor_560

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_2:1148160..1148791(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIE
• Ensembl ID: ENSCPOG00000007365
• Aliases: None
• Description: None

Sequence

>retro_cpor_560
TTTATTCTTTTTGGAGACACCACAGACACTCAGAGTCCTCTGGATTATAAAGCAGAAAAGCATCGAGGATTTGCTTTTGA
TGGATTTGAGTTGGCAGAGGATGCAGCAGCAGCTATTGACAACACGAATGAATCTGAGCTCTTTGGAGGGACAATTCATG
TCAATTCGGCCAAACAAGGAGAATTAGAGGGCTCTTCTAGACCAGTGTTGTCAGACGATGATGACTGATGGAAGAAGTTT
TATGGAAGACTCTTATGGGAAGAGGAAGAAGGGAAAGAAACTCCCAAAGCAGAAACCCAGGAAGAAGAGGACCCCTCTGC
AAAAAAGGCCGGGTCAAACCCTCAGGTGTACATGGCGTCAAGATCAGGAGCAAGCCAGCCTGCCACCTCCAGATGCGCCT
GCGTTCTGACCTCGTGTCCACGACCCGGGAGACTTTCTGCAGCCTGAGTGCCCACGGAAAAGGCTATGGCTTCAGGGGAA
GTAGCTTCCACCGCAACATCCACCAGTTCATGTGCCAGGGTGGGAATTTCACAAACCACAGTGCCACTGGGGCAAGTCCA
TCTCCTGGAAGACGTTTGATGACGAAAACTTTATCCTTAAACACACAGGACTAGACCTCCTCGCCATGGCC

Alignment

ORF - retro_cpor_560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.64 %
• Parental protein coverage: 70.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FIPFGDITDIQIPLDYETAEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKEGSSRP
          FI.FGD.TD.Q.PLDY..AEKHRGFAF..FELAEDAAAAIDN.NESELFG.TI.VN.AK.....EGSSRP
Retrocopy FILFGDTTDTQSPLDYK-AEKHRGFAFDGFELAEDAAAAIDNTNESELFGGTIHVNSAKQGEL-EGSSRP

Parental  VWSDDD--WLKKFSGKTLEENKEEEGTETPKAETQEGEPP-AKKARSNPQVYM-DIKIGNKPAGRIQMLL
          V.SDDD..W.KKF.G..L.E..EEEG.ETPKAETQE.E.P.AKKA.SNPQVYM...KI..KPA...QM.L
Retrocopy VLSDDDD*W-KKFYGRLLWE--EEEGKETPKAETQEEEDPSAKKAGSNPQVYM<GVKIRSKPACHLQMRL

Parental  RSDVVPMTAENFRCLCTHEKGYGFKGSSFHRIIPQFMCQGGDFTNHNGTG-GKSIYGKKFDDENFILKHT
          RSD.V..T.E.F..L..H.KGYGF.GSSFHR.I.QFMCQGG.FTNH..TG.GKSI..K.FDDENFILKHT
Retrocopy RSDLVSTTRETFCSLSAHGKGYGFRGSSFHRNIHQFMCQGGNFTNHSATG<GKSISWKTFDDENFILKHT

Parental  GPGLLSMA
          G..LL.MA
Retrocopy GLDLLAMA

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	10.81 RPM
SRP017611_kidney	0.00 RPM	16.96 RPM
SRP017611_liver	0.00 RPM	13.41 RPM
SRP040447_lung	0.03 RPM	20.45 RPM
SRP040447_skeletal_muscle	0.00 RPM	13.36 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_560 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_560 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 6 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000002632	11 retrocopies	retro_cpor_1152, retro_cpor_1284, retro_cpor_1395, retro_cpor_1493, retro_cpor_165, retro_cpor_192, retro_cpor_251, retro_cpor_372, retro_cpor_642, retro_cpor_902, retro_cpor_960,
Cavia porcellus	ENSCPOG00000007365	1 retrocopy	retro_cpor_560 ,
Myotis lucifugus	ENSMLUG00000016233	1 retrocopy	retro_mluc_339,
Tursiops truncatus	ENSTTRG00000014385	1 retrocopy	retro_ttru_1314,
Vicugna pacos	ENSVPAG00000010049	2 retrocopies	retro_vpac_261, retro_vpac_86,
Xenopus tropicalis	ENSXETG00000018981	1 retrocopy	retro_xtro_20,