RetrogeneDB ID: retro_cpor_324

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_125:1710237..1710899(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL3
• Ensembl ID: ENSCPOG00000021216
• Aliases: None
• Description: None

Sequence

>retro_cpor_324
ATGCCAGGTTGGAAGTTACTGGAACAGGTGGGCATCCAGTTTTCGGGCTGCAGCACTGGCAGCTTGGGTGCTACCTTCAG
CTTGGGGAGAACAAACATGGGGCTTTCTGTTGGAGGTCTCTCTGGTAGGAACCCAAGTTGGTGAGATGATCATCTTTCTG
AAGAAAAACCTCATTTGCTAAGCAGCTGGTCTCTGATAAAGACCAAGCCCAGTGAGCAAGTAAAGTATGTCCTCTAAAAG
ACGAACCGTGGCCTATACATCCTCGGGAACGAGGTTCTTCTAGAGTTGACCTTATTGCCCTGAAGTGGGCATGATGCTTT
TAGGGACTTCGGATGGTCCAAAGCATGTAGTCACATTACTACAGGCACAAGATTGTCATGTTTGAAAATACGCTTCAAAG
GAAAGCCACAATGGAAAGATGGCAGCCCTGACTGTAGGAAGGAAAACTGGGTCGCTTTTCCGTAAATCTGAACCTGCATT
GGAATTTTACCAAGACCTTGGATTGCCACCAAAACAGAAAGTTAAAACTTGTCGAGTAACAGATCATGCTTGTAATTAAA
CCAGGCACTCCTCCCTACGCGGCTCGCTTTCATCCAGAACAGCATGGGGATGTCACCACCAAAACTATTGGTAAAGGTTT
TCAGGGCGTCATGAAAAGATGG

Alignment

ORF - retro_cpor_324 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.22 %
• Parental protein coverage: 63.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPGWRLLAQAGAQFLGCSTGGLAAAPGLRSRTNIWLFVRSLHDKSPTWWDEHLSEEN-TSFVKKLVSDED
          MPGW.LL.Q.G.QF.GCSTG.L.A...L..RTN..L.V..L....P.W.D.HLSEE..TSF.K.LVSD.D
Retrocopy MPGWKLLEQVGIQFSGCSTGSLGATFSL-GRTNMGLSVGGLSGRNPSW*DDHLSEEK<TSFAKQLVSDKD

Parental  KAQLASKLCPLKDEPWPINPWEPGSSRVGLIALK-LGMMPLWTKDGQKHAVTLLQVQDCHVLKYTSKENH
          .AQ.ASK.CPLKDEPWPI.P.E.GSSRV.LIALK..GMM.L.T.DG.KH.VTLLQ.QDCHV.KY.SKE.H
Retrocopy QAQ*ASKVCPLKDEPWPIHPRERGSSRVDLIALK<VGMMLLGTSDGPKHVVTLLQAQDCHV*KYASKESH

Parental  NGKMAALTVGGKTVSRFRKSESVLEFYRELGLPPKQTVKIFHVTDNA-VIKPGTPLYAAHFRPGQYVDVT
          NGKMAALTVG.KT.S.FRKSE..LEFY..LGLPPKQ.VK...VTD.A.VIKPGTP.YAA.F.P.Q..DVT
Retrocopy NGKMAALTVGRKTGSLFRKSEPALEFYQDLGLPPKQKVKTCRVTDHA>VIKPGTPPYAARFHPEQHGDVT

Parental  AKTIGKGFQGVMKRW
          .KTIGKGFQGVMKRW
Retrocopy TKTIGKGFQGVMKRW

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	22.09 RPM
SRP017611_kidney	0.00 RPM	48.16 RPM
SRP017611_liver	0.00 RPM	26.59 RPM
SRP040447_lung	0.00 RPM	20.45 RPM
SRP040447_skeletal_muscle	0.00 RPM	26.90 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_324 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_324 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000021216	1 retrocopy	retro_cpor_324 ,
Dasypus novemcinctus	ENSDNOG00000014498	1 retrocopy	retro_dnov_178,
Homo sapiens	ENSG00000114686	1 retrocopy	retro_hsap_1236,
Gorilla gorilla	ENSGGOG00000011128	1 retrocopy	retro_ggor_969,
Microcebus murinus	ENSMICG00000009524	1 retrocopy	retro_mmur_1106,
Ochotona princeps	ENSOPRG00000000501	1 retrocopy	retro_opri_589,
Pan troglodytes	ENSPTRG00000015396	1 retrocopy	retro_ptro_850,
Sus scrofa	ENSSSCG00000011179	1 retrocopy	retro_sscr_126,