RetrogeneDB ID: retro_cpor_303

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_12:28569789..28570250(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC20
• Ensembl ID: ENSCPOG00000011489
• Aliases: None
• Description: None

Sequence

>retro_cpor_303
GATTATCACAGTCCCACAGTGAATAACTGCGGGATTTTCTAATCACAAATTTTTCGTGCTGCGTTTACTGTGTTTTCTGT
TATATTGGCTTTTTGTTCAACAGTTTTAGAATATTTTAATATTTGGAAGAGTGTACTGACAGATACGAACAAAATTCCAC
TTTTCCTTTTCTTTGTGTCTGTAATGCTCTTCCTCCATGTCCTCTGGCTGTTCGGGTACCACTGCTGGCTAGTTGAAAAA
AATAGAACAACTATAGAATCATTCCGTTCACCTATGTTTTCATATGGACCTGATGGGAATCGTTCCTCTGTCAGCTACAG
TAAAAATTGGAGATAAGTATTTGGCGACGAAAAGAAATACTGGCTACTCCAGTGTTTTCAAGCTTGGGTGATGGTTGCAG
TTTCCCAACTTGCCAAGAGGGGACGGATCTAGAACAAGCTTCTGGAACAAACCAAAATGAA

Alignment

ORF - retro_cpor_303 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 51.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DHHCPWVNNCVGFSNYKFFMLFLLYSLLYCLFVATTVLEYFIKFWTNELTDTRAKFHVLFLFFVSAMFFI
          D.H.P.VNNC..F....F...F...S....L....TVLEYF...W...L..T......LFLFFVS.M.F.
Retrocopy DYHSPTVNNCGIF*SQIFRAAFTVFSVI--LAFCSTVLEYF-NIWKSVL--TDTNKIPLFLFFVSVMLFL

Parental  SVLSLFSYHCWLVGKNRTTIESFRAPTFSYGPDGNGFSLGYTKNWRQVFGEEKKYWLL-PVFSSLGDGCS
          .VL.LF.YHCWLV.KNRTTIESFR.P.FSYGPDGN..S..Y.KNWR.VFG.EKKYWLL.PVFSSLGDGCS
Retrocopy HVLWLFGYHCWLVEKNRTTIESFRSPMFSYGPDGNRSSVSYSKNWR*VFGDEKKYWLL<PVFSSLGDGCS

Parental  FPTRLVGMDPEQASGTNQND
          FPT...G.D.EQASGTNQN.
Retrocopy FPTCQEGTDLEQASGTNQNE

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	0.35 RPM	15.64 RPM
SRP017611_kidney	0.10 RPM	15.49 RPM
SRP017611_liver	0.00 RPM	19.98 RPM
SRP040447_lung	0.15 RPM	25.45 RPM
SRP040447_skeletal_muscle	0.05 RPM	5.24 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_303 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_303 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012155	2 retrocopies	retro_chof_1627, retro_chof_2008,
Cavia porcellus	ENSCPOG00000011489	1 retrocopy	retro_cpor_303 ,
Equus caballus	ENSECAG00000016465	1 retrocopy	retro_ecab_683,
Homo sapiens	ENSG00000180776	1 retrocopy	retro_hsap_1211,
Gorilla gorilla	ENSGGOG00000000435	2 retrocopies	retro_ggor_1003, retro_ggor_943,
Macaca mulatta	ENSMMUG00000007373	1 retrocopy	retro_mmul_1288,
Pongo abelii	ENSPPYG00000005201	1 retrocopy	retro_pabe_1081,
Pan troglodytes	ENSPTRG00000005695	1 retrocopy	retro_ptro_829,
Tarsius syrichta	ENSTSYG00000003013	1 retrocopy	retro_tsyr_998,