RetrogeneDB ID: retro_cpor_999

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_39:15914111..15914804(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RCL1
• Ensembl ID: ENSCPOG00000015354
• Aliases: None
• Description: None

Sequence

>retro_cpor_999
AACAGGAACAACCTTATCCAGTACTATCAGCCTGGCTTCCTGAATTATGGATCTGTGAAACATGACACTAATGTCCTTTG
CAGCATTAGCTATAATGTGGAGGTTCTCTTTTGCCTGGCTCCATTTATGAAGCACCTATTAGAAATAGTTCTTCAAGGAA
TGACCGCTGACCACATTTATCCTTTGGTTGATGTTCGTAAGGCAACAGCACTCCTTCTATTGAAACAGTTTGGGATTGAT
GGTAAATTGCTCTAACAAAAGTTTATTCAACAAGGAATGCCTCCTGGAAAAGGAGGTGAAGTGGTTTTCTCCTGTCCTAT
CAGGAAGGTCCCGGAAGTCCATTCAGGTCAAGATTCCAGGAAAAATCAAATGTACAGAGGAATGGCATATTTAGTACATA
TGTCACCTTAGATAGCAAACTGGATTGTGGATTCTGCAAGGAGCATCCTCAATCAGCTCGTGCCCAGTCTCTGTACTTAC
ACAGACCACATGAGAGAAGCTGATGCTGCAAGTCTTCAGGCTTTGAGTTATCCCTGGTTTCTTAGACCACAGTGGCACTT
CCTTAGTGCTAACCTGACCTCCAATGCCCAGAGCCAAGGAGCAGCTGTGCTTTCAGAGGAGTTTGGGAGGAACTATGCCC
AGCTGCTGCTTGAAGAGATCCACAGAGGTGCATGTGTAGACTTAGGCAACCAA

Alignment

ORF - retro_cpor_999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.03 %
• Parental protein coverage: 62.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  NQTGTTLYYQPGLLYGGPVEHDCSVLRSIGYYLEGLLCLAPFMKHPLKIVLRGVTNDQIDPSVDVLKATA
          N......YYQPG.L..G.V.HD..VL.SI.Y..E.L.CLAPFMKH.L.IVL.G.T.D.I.P.VDV.KATA
Retrocopy NRNNLIQYYQPGFLNYGSVKHDTNVLCSISYNVEVLFCLAPFMKHLLEIVLQGMTADHIYPLVDVRKATA

Parental  LPLLKQFGIDGESFELKIVRRGMPPGGGGEVFFSCPVRKV-LKPIQLTDPGKIK-RIRGMAYSVRVSPQM
          L.LLKQFGIDG.....K....GMPPG.GGEV.FSCP.RKV..K.IQ...PGKIK...RGMAY.V..SP..
Retrocopy LLLLKQFGIDGKLL*QKFIQQGMPPGKGGEVVFSCPIRKV>RKSIQVKIPGKIK<MYRGMAYLVHMSP*I

Parental  ANRIVDSARSILNKFIPDIYIYTDHMKGVNSG-KSPGFGLSLVAETT-NGT-FLSAELASNPQGQGTAVL
          AN.IVDSARSILN...P....YTDHM.......KS.GF.LSLV..TT..GT.FLSA.L.SN.Q.QG.AVL
Retrocopy ANWIVDSARSILNQLVPSLCTYTDHMREADAA<KSSGFELSLVS*TT<SGT<FLSANLTSNAQSQGAAVL

Parental  PEDLGRNCARLLLEEIHRGGCVDSTNQ
          .E..GRN.A.LLLEEIHRG.CVD..NQ
Retrocopy SEEFGRNYAQLLLEEIHRGACVDLGNQ

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	5.75 RPM
SRP017611_kidney	0.10 RPM	13.61 RPM
SRP017611_liver	0.04 RPM	53.41 RPM
SRP040447_lung	0.08 RPM	12.36 RPM
SRP040447_skeletal_muscle	0.01 RPM	9.22 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_999 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_999 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000015354	1 retrocopy	retro_cpor_999 ,