RetrogeneDB ID: retro_cpor_595

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_2:13541275..13542071(-)
• Located in intron of: ENSCPOG00000007324

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYP2R1
• Ensembl ID: ENSCPOG00000015305
• Aliases: None
• Description: None

Sequence

>retro_cpor_595
AGTGCCTTTCCATGGATTGGCTTCTTGCCTTTTGGAAAACATCAACAGCTGTTTAGAAATGCAGCTATGGTCTATGATTT
TCTCTCCAGACTTACTGAAAAAGCTTCAGTAAACAGAAAACTTTAGGTACCTCAGCATTTTGTTGATGCTTATGTAGACT
AAATGGATCAAGGTAAAAATGACCCATCATCTACCTTCTCCAAAGAAAACCTAATTTTCTGAGGGGTGATCTTATCATTG
CTGGAACTGAAACTACAACCAATGTTCTATGCTGGGCAATTATTTTCACGGCCCTTTATCCCAACATTCAAGGACAAGTT
TGAAAAGAGATTGATTTGGTAATGGGCCCAAATAGACAGCCTTCTTGGTATGAAAAATGCAAAAGGCCATACACTAAAGC
AGTTTTGCATGAAGTTTTAAGATTCTGCTATATAGTTCCATTAGGGATTTTCCACGCAGTCTCTGAAGATGCAGTCATAT
GTGGTTATTCCATTCTAAAAGGCACAATGATAATTACAAATCCTAATTCTGTACACTTTGATGGAAAGTACCGGAGAGAC
CCAGAAGTGTTCTATCCTGAACAATTTCTAAACAGTAGTGGATATTTTGTAAAAAAGAAAGCTTTGGTTCCTTTTTCCTT
AGGGAAAAGACATTGTCTTGGAGAACAGCAGGCTCAAATGGAAATGTTTTTTACAGCATTGCTTTAGCAGTTTCATTTGC
ATTTTCCACATGAACTACTTCCAAATCTGAAGCCCAGGTTAGGGATGACATTGTAGCCCAGCCTTACCTCATCTGT

Alignment

ORF - retro_cpor_595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.26 %
• Parental protein coverage: 53.49 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NAFPWIGILPFGKHHQLFKNAAVVSDFLSRLIEKASVNRKPQLPRHFVDAYLDEMDQGKNDPSSTFSKEN
          .AFPWIG.LPFGKH.QLF.NAA.V.DFLSRL.EKASVNRK...P.HFVDAY.D.MDQGKNDPSSTFSKEN
Retrocopy SAFPWIGFLPFGKHQQLFRNAAMVYDFLSRLTEKASVNRKL*VPQHFVDAYVD*MDQGKNDPSSTFSKEN

Parental  LIF-SVGELIIAGTETTTNVLRWAILFMALYPNIQGQVWKEIDLIMGPNRQPSWDDKCKMPYTEAVLHEV
          LIF...G.LIIAGTETTTNVL.WAI.F.ALYPNIQGQV.KEIDL.MGPNRQPSW..KCK.PYT.AVLHEV
Retrocopy LIF<LRGDLIIAGTETTTNVLCWAIIFTALYPNIQGQV*KEIDLVMGPNRQPSWYEKCKRPYTKAVLHEV

Parental  LRFCNIVPLGIFHATSEDAVVRGYSIPKGTTVITNLYSAHFDEKYWRDPEVFYPERFLDSSGDFVKKEAL
          LRFC.IVPLGIFHA.SEDAV..GYSI.KGT..ITN..S.HFD.KY.RDPEVFYPE.FL.SSG.FVKK.AL
Retrocopy LRFCYIVPLGIFHAVSEDAVICGYSILKGTMIITNPNSVHFDGKYRRDPEVFYPEQFLNSSGYFVKKKAL

Parental  VPFSLGRRHCLGEQLARMEMFLFFTALLQRFHLHFPQDLVPNLMPRLGMTLQP-QPYLVC
          VPFSLG.RHCLGEQ.A.MEM..FFTALL..FHLHFP..L.PNL.PRLGMTL.P.QPYL.C
Retrocopy VPFSLGKRHCLGEQQAQMEM--FFTALL*QFHLHFPHELLPNLKPRLGMTL*P<QPYLIC

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	0.92 RPM
SRP017611_kidney	0.00 RPM	12.77 RPM
SRP017611_liver	0.00 RPM	8.05 RPM
SRP040447_lung	0.00 RPM	1.24 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.02 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_595 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_595 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000015305	1 retrocopy	retro_cpor_595 ,
Equus caballus	ENSECAG00000007597	1 retrocopy	retro_ecab_128,
Ochotona princeps	ENSOPRG00000006268	1 retrocopy	retro_opri_1208,