RetrogeneDB ID: retro_cpor_337

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_13:20290600..20291072(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD10
• Ensembl ID: ENSCPOG00000020474
• Aliases: None
• Description: None

Sequence

>retro_cpor_337
TCCATTACCCTGATCCTGCCCAACAGCCCCAACATGAAAAGAGCAATGTCATTGATACATGCACTAGACATAGGAAGACT
GCCAAGACTGCTTACCTGATTGTTCAAAACCCTCACCCAAAGCCTAAGAGCACTCTCAGTGAAGATAAAGAAGAAAAACT
TTAAGCGCACTTTCTCTAGAGAAATAAGATCTCTTCACCTAGTTCTTGAAACAATATCATTATTTCAGAATATGCATACA
TCACAATGTGAAGCCAATACCTTTACCACAGCAATTAGAGAGCGTTCATCTTGTACAAAACAAACCAGAAACATTTGTCA
GTGCTTGGTCTCCTATGAGTCAAGAGACAGCTGAAAAGTTCAAGCAAAACATTTTGCTTCCCCACGAGTTAGAGACATTT
GGATGGCAGTTTAACCTTCAAATAGCTCCCTCTGCCTTTGCAAAACAAAAATCTCCTCCAGCTAAATTAAAA

Alignment

ORF - retro_cpor_337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.76 %
• Parental protein coverage: 93.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SAVLILPNSPSMKKAVLLINALDTGRFPRLLT-RILQKLHLKAESSFNEDEEEKLQA-AFSLEKQELHLV
          S..LILPNSP.MK.A..LI.ALD.GR.PRLLT..I.Q..H.K..S...ED.EEKL.A..FS.E...LHLV
Retrocopy SITLILPNSPNMKRAMSLIHALDIGRLPRLLT<LIVQNPHPKPKSTLSEDKEEKL*A>TFSREIRSLHLV

Parental  LETISF-ILEQA-VYHNVKPAALQQQLENIHLEQDKAEAFVNVWSSMGQETVEKFRQRVLAPHKTKLETV
          LETIS..I.E.A...HNVKP..L.QQLE..HL.Q.K.E.FV..WS.M.QET.EKF.Q..L.PH...LET.
Retrocopy LETISL<ISEYA<IHHNVKPIPLPQQLESVHLVQNKPETFVSAWSPMSQETAEKFKQNILLPH--ELETF

Parental  GWQLNLQMAHSAQAKLKSPQVVLQ
          GWQ.NLQ.A.SA.AK.KSP...L.
Retrocopy GWQFNLQIAPSAFAKQKSPPAKLK

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	7.42 RPM
SRP017611_kidney	0.00 RPM	8.37 RPM
SRP017611_liver	0.00 RPM	6.44 RPM
SRP040447_lung	0.00 RPM	6.66 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.76 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_337 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_337 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008311	2 retrocopies	retro_chof_1462, retro_chof_1585,
Cavia porcellus	ENSCPOG00000020474	1 retrocopy	retro_cpor_337 ,
Loxodonta africana	ENSLAFG00000011885	1 retrocopy	retro_lafr_142,
Microcebus murinus	ENSMICG00000006173	2 retrocopies	retro_mmur_1132, retro_mmur_607,
Myotis lucifugus	ENSMLUG00000010780	1 retrocopy	retro_mluc_2087,
Sarcophilus harrisii	ENSSHAG00000001698	1 retrocopy	retro_shar_261,
Tupaia belangeri	ENSTBEG00000004061	1 retrocopy	retro_tbel_3381,