RetrogeneDB ID: retro_cpor_1252

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_6:31956973..31957299(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEAF6
• Ensembl ID: ENSCPOG00000025988
• Aliases: None
• Description: None

Sequence

>retro_cpor_1252
AAAGACACTCAGATGAATGGCAATGTTATTCATGGTCAGGATCGGTATCTGACAACCAAAAAGCTCCAATAATAATAACA
GCAAACGACAGAAGGAACTGGAAGCCGAGCAGCTGTTCAGTGAATCAGCTGCTTTCGTGGCAGGTGTAGTGAGCGCACTG
CCAGAGGTTCAGGACCAGCTCACTGAAAAGGGGGAGCCAGGAAGTGGAACGCAAAGTGACTACCTGCCCGGATTTGCGCC
AGGAGGACCGTGAGGATCCGGAGAGATTCGTGCAGACAGCCAAACGCTAAGGGGGTTCTTCGCCCTCCTCAGGGAGTCAT
CACAGC

Alignment

ORF - retro_cpor_1252 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.89 %
• Parental protein coverage: 73.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EDTQMYGNIIRGWDRYLT-NQK-NSNSKNDRRNRKFKEAERLFSKSSVTSAAAVSALAGVQDQLIEKREP
          .DTQM.GN.I.G.DRYLT.NQK..SN..N..R.....EAE.LFS.S....A..VSAL..VQDQL.EK.EP
Retrocopy KDTQMNGNVIHGQDRYLT<NQK<SSNNNNSKRQKEL-EAEQLFSESAAFVAGVVSALPEVQDQLTEKGEP

Parental  GSGTESD-TSPDFHNQENEPSQEDPEDLDGSVQGVKPQKAASSTSSGSHHS
          GSGT.SD.T.PD......E....DPE.....VQ..K.....S..S.GSHHS
Retrocopy GSGTQSD>TCPDLRQEDRE----DPERF---VQTAKR*GGSSPSS-GSHHS

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	15.53 RPM
SRP017611_kidney	0.00 RPM	8.06 RPM
SRP017611_liver	0.00 RPM	5.75 RPM
SRP040447_lung	0.00 RPM	13.37 RPM
SRP040447_skeletal_muscle	0.00 RPM	5.18 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1252 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1252 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001927	1 retrocopy	retro_cjac_2767,
Cavia porcellus	ENSCPOG00000025988	1 retrocopy	retro_cpor_1252 ,
Erinaceus europaeus	ENSEEUG00000013971	3 retrocopies	retro_eeur_362, retro_eeur_469, retro_eeur_654,
Macropus eugenii	ENSMEUG00000003403	3 retrocopies	retro_meug_1279, retro_meug_584, retro_meug_727,
Myotis lucifugus	ENSMLUG00000017128	2 retrocopies	retro_mluc_436, retro_mluc_960,
Otolemur garnettii	ENSOGAG00000006773	1 retrocopy	retro_ogar_2339,
Vicugna pacos	ENSVPAG00000001916	1 retrocopy	retro_vpac_566,