RetrogeneDB ID: retro_cpor_1036

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:24359461..24359844(-)
• Located in intron of: ENSCPOG00000008536

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000002251
• Aliases: None
• Description: None

Sequence

>retro_cpor_1036
TCGCCCTCCAACCAGCAAACCAAGGAAGAAACAAACACCCCAAAGAAGGAGAGTAAAGTCAGCATAAGCAGAAACTCCAA
GCTCCTCTCTACCAGCGCCAAGAGGATTCAGAAGGAGCTGGCAGACATCACTCTAAACCCTCTATCTAACTGCAGTGCTA
GTCCCAAAGGTGATAACATCTATGAGTGGAGATCTACCATTCTAGGACCTCCAAGATCTGTGTATGAAGGTGGTATATTT
TTCCTAGATATCACTTTTACTCCAGAATATCCCTTCAAACCTCCAAAGGTTACATTTCAGACACCAATCTATCACTGCAA
TACTAACAGTCAAAGAGTTATTGCTTGGATATAATGAAAGATAATTATAGTCCAACAATAAGT

Alignment

ORF - retro_cpor_1036 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.08 %
• Parental protein coverage: 66.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSSNQQTEKETNTPKKKESKVSMSKNSKLLSTSAKRIQKELADITLDPPPNCSAGPKGDNIYEWRSTILG
          S.SNQQT..ETNTPKK.ESKVS.S.NSKLLSTSAKRIQKELADITL.P..NCSA.PKGDNIYEWRSTILG
Retrocopy SPSNQQTKEETNTPKK-ESKVSISRNSKLLSTSAKRIQKELADITLNPLSNCSASPKGDNIYEWRSTILG

Parental  PPGSVYEGGVFFLDITFTPEYPFKPPKVTFRTRIYHCNINSQGVI-CLDILKDNWSPALT
          PP.SVYEGG.FFLDITFTPEYPFKPPKVTF.T.IYHCN.NSQ.VI.CLDI.KDN.SP...
Retrocopy PPRSVYEGGIFFLDITFTPEYPFKPPKVTFQTPIYHCNTNSQRVI<CLDIMKDNYSPTIS

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	15.87 RPM
SRP017611_kidney	0.00 RPM	11.93 RPM
SRP017611_liver	0.00 RPM	7.14 RPM
SRP040447_lung	0.00 RPM	23.88 RPM
SRP040447_skeletal_muscle	0.00 RPM	14.63 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1036 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1036 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 17 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003515	2 retrocopies	retro_amel_1117, retro_amel_483,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Cavia porcellus	ENSCPOG00000002251	2 retrocopies	retro_cpor_1036 , retro_cpor_52,
Cavia porcellus	ENSCPOG00000006044	2 retrocopies	retro_cpor_692, retro_cpor_835,
Dipodomys ordii	ENSDORG00000015441	1 retrocopy	retro_dord_785,
Felis catus	ENSFCAG00000024719	1 retrocopy	retro_fcat_623,
Gorilla gorilla	ENSGGOG00000008393	1 retrocopy	retro_ggor_76,
Loxodonta africana	ENSLAFG00000004150	1 retrocopy	retro_lafr_320,
Macropus eugenii	ENSMEUG00000014517	1 retrocopy	retro_meug_2089,
Mus musculus	ENSMUSG00000021774	3 retrocopies	retro_mmus_2493, retro_mmus_2600, retro_mmus_537,
Oryctolagus cuniculus	ENSOCUG00000006026	2 retrocopies	retro_ocun_134, retro_ocun_243,
Otolemur garnettii	ENSOGAG00000007527	3 retrocopies	retro_ogar_2029, retro_ogar_2566, retro_ogar_626,
Pan troglodytes	ENSPTRG00000014693	1 retrocopy	retro_ptro_68,
Pteropus vampyrus	ENSPVAG00000001773	1 retrocopy	retro_pvam_1451,
Rattus norvegicus	ENSRNOG00000008794	3 retrocopies	retro_rnor_1632, retro_rnor_2291, retro_rnor_2343,
Sarcophilus harrisii	ENSSHAG00000001416	1 retrocopy	retro_shar_712,
Ictidomys tridecemlineatus	ENSSTOG00000025799	2 retrocopies	retro_itri_1371, retro_itri_645,