RetrogeneDB ID: retro_cpor_489

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_17:17215717..17215966(+)
• Located in intron of: ENSCPOG00000005628

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2A
• Ensembl ID: ENSCPOG00000011908
• Aliases: None
• Description: None

Sequence

>retro_cpor_489
ATGTCCACTCCGGCTTGGCAGCACCTAATGAGGTGCTGCAAGAGGCTGCAGGAAGATCCTCTGGCTGGAGTCAGCGGGGC
TCCATCAGAGAACAACATAATGGTTTGGAACGCAGTCATTTTCCGGCCTGAAGGGACCCCATTTGAGAATGAAACATTTA
AATTTATAATAGAATTCACTGAAGAGCATCTGAATAAACTACCTACAGTTAGATTTATCTCTAAGATGTTTCATTCAAAT
GTCTATGCA

Alignment

ORF - retro_cpor_489 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.93 %
• Parental protein coverage: 54.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTPARRRLMRDFKRLQEDPPAGVSGAPSENNIMVWNAVIFGPEGTPFEDGTFKLTIEFTEEYPNKPPTV
          MSTPA...LMR..KRLQEDP.AGVSGAPSENNIMVWNAVIF.PEGTPFE..TFK..IEFTEE..NK.PTV
Retrocopy MSTPAWQHLMRCCKRLQEDPLAGVSGAPSENNIMVWNAVIFRPEGTPFENETFKFIIEFTEEHLNKLPTV

Parental  RFISKMFHPNVYA
          RFISKMFH.NVYA
Retrocopy RFISKMFHSNVYA

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	20.25 RPM
SRP017611_kidney	0.00 RPM	14.87 RPM
SRP017611_liver	0.00 RPM	18.72 RPM
SRP040447_lung	0.00 RPM	15.21 RPM
SRP040447_skeletal_muscle	0.00 RPM	18.42 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_489 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_489 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001079	1 retrocopy	retro_chof_1316,
Callithrix jacchus	ENSCJAG00000005098	2 retrocopies	retro_cjac_1180, retro_cjac_3862,
Cavia porcellus	ENSCPOG00000011908	1 retrocopy	retro_cpor_489 ,
Dasypus novemcinctus	ENSDNOG00000007060	1 retrocopy	retro_dnov_215,
Macropus eugenii	ENSMEUG00000003026	1 retrocopy	retro_meug_2180,
Monodelphis domestica	ENSMODG00000010209	1 retrocopy	retro_mdom_341,
Oryctolagus cuniculus	ENSOCUG00000016739	1 retrocopy	retro_ocun_183,
Otolemur garnettii	ENSOGAG00000024335	1 retrocopy	retro_ogar_3203,
Procavia capensis	ENSPCAG00000005045	1 retrocopy	retro_pcap_222,
Sus scrofa	ENSSSCG00000012621	1 retrocopy	retro_sscr_29,
Tarsius syrichta	ENSTSYG00000000888	1 retrocopy	retro_tsyr_676,