RetrogeneDB ID: retro_cpor_734

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_26:862582..863191(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSGEP
• Ensembl ID: ENSCPOG00000014460
• Aliases: None
• Description: None

Sequence

>retro_cpor_734
CTTCTGGCCTATTTTGCAAGCAGAACCAAGATTGGCGTGGGAGTTCTGAAGGATGGTGAGGTTCTGACAAACCCACTGAA
AACCCATGCTACACCTCCAGGCATAGGATTCCTCCCAAGTACTACTGCTAGGCACCACGGAACTATTATCCTAGGATTGC
GGCAGGAAGAACTAACAGAAGCCAGATTAACTTCCCAAGATATCAATTGCATTGCTTACACCAAAGGCCCTAGCATGGGT
ACCCACTGGCTTCCATAGCAGTTGTGGCCCATATGGTGGCTCCGCTGTGGAATAAACCTCTGGAAGCTGTGAACCACTGT
ATAGACCACATTAAAATGGGCGGCCTCATCACTGGGGCCACCAGCCAACTGTAGTATAAGTCAGCAGAGGAAATACTCAG
GTCATTACCTACTCAGAACATCAGTACTGAATCTTTGGGGAAATCATTGATACTGCTGTGGTAATTCTCTGATCACTTTG
TTTGAGTGCTAAAGATTTCCAATGATCCAAGTCCAGGTTACAACGTTACAACAGATGGCAAAACGAGGCTGGAAGCTAGT
TGAGCTGCCATACATTGTAAAGGGGATGGATGTCTCATTTTCAGGGATT

Alignment

ORF - retro_cpor_734 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.77 %
• Parental protein coverage: 63.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VLGFEGSANKIGVGVVRDGKVLANPRRTYVTPPGTGFLPGATARHHRAVILDLLQEALTEAGLTSQDIDC
          .L....S..KIGVGV..DG.VL.NP..T..TPPG.GFLP..TARHH...IL.L.QE.LTEA.LTSQDI.C
Retrocopy LLAYFASRTKIGVGVLKDGEVLTNPLKTHATPPGIGFLPSTTARHHGTIILGLRQEELTEARLTSQDINC

Parental  IAYTKGPGMGA-PLASVAVVARTVAQLWNKPLVGVNHCIGHIEMGRLITGATS-PTVLYVSGGNTQVIAY
          IAYTKGP.MG..PLAS.AVVA..VA.LWNKPL..VNHCI.HI.MG.LITGATS.PTV..VS.GNTQVI.Y
Retrocopy IAYTKGPSMGT<PLASIAVVAHMVAPLWNKPLEAVNHCIDHIKMGGLITGATS<PTVV*VSRGNTQVITY

Parental  SEHRYRIFGETIDIAV-GNCL-DRFARVLKISNDPSPGYNI-EQMAKCGKKLVELPYTVKGMDVSFSGI
          SEH.Y.IFGE.ID.AV.GN.L.D.F..VLKISNDPSPGYN...QMAK.G.KLVELPY.VKGMDVSFSGI
Retrocopy SEHQY*IFGEIIDTAV<GNSL<DHFV*VLKISNDPSPGYNV>QQMAKRGWKLVELPYIVKGMDVSFSGI

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	8.68 RPM
SRP017611_kidney	0.00 RPM	15.07 RPM
SRP017611_liver	0.00 RPM	8.57 RPM
SRP040447_lung	0.00 RPM	19.80 RPM
SRP040447_skeletal_muscle	0.00 RPM	7.67 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_734 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_734 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014460	1 retrocopy	retro_cpor_734 ,
Mus musculus	ENSMUSG00000006289	1 retrocopy	retro_mmus_1765,
Oryctolagus cuniculus	ENSOCUG00000005020	1 retrocopy	retro_ocun_562,