RetrogeneDB ID:

retro_cpor_304

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_12:28677666..28677911(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCPOG00000000429
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_304
TGTGTGCTTGCATCCAACTGTAATGAGCCTGAGAATGGCGAGTTGGTAGAGGCCCTTTGTGCTGAGCACATCAACCTAAT
TAAAGCTGATGGCAACAAGAAACTGAGGGAATGAATAAGGCTTGTAAAATTGACTAAGAGGGGAAGCTGCGTAAAATGGT
TGATTGTACTTGTGTAGTGGTTAAGAACTATGGCAAAGAATTTCAAGCCAAAGATGTCATCAAACTGTACTTCAAATCCA
AGAAA

ORF - retro_cpor_304 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.76 %
Parental protein coverage: 63.16 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalCVLASNCDEPMYVKLVEALCAEHQINLIKVDDNKKLGEWVGL-CKIDREGKPRKVVGCSCVVVKKDYGKE
CVLASNC.EP....LVEALCAEH.INLIK.D.NKKL.E...L.CKID.EGK.RK.V.C.CVVV.K.YGKE
RetrocopyCVLASNCNEPENGELVEALCAEH-INLIKADGNKKLRE*IRL<CKID*EGKLRKMVDCTCVVV-KNYGKE
ParentalSQAKDVIEEYFKCKK
.QAKDVI..YFK.KK
RetrocopyFQAKDVIKLYFKSKK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP017611_brain 0 .00 RPM 77 .13 RPM
SRP017611_kidney 0 .00 RPM 149 .39 RPM
SRP017611_liver 0 .00 RPM 112 .78 RPM
SRP040447_lung 0 .00 RPM 294 .81 RPM
SRP040447_skeletal_muscle 0 .00 RPM 267 .11 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_304 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_304 was not experimentally validated.

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.

Parental genes homology:
Parental genes homology involve 36 parental genes, and 363 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000104791 retrocopy
Ailuropoda melanoleuca ENSAMEG000000080152 retrocopies
Bos taurus ENSBTAG000000013607 retrocopies
Canis familiaris ENSCAFG0000000019015 retrocopies
Callithrix jacchus ENSCJAG0000000286534 retrocopies
Cavia porcellus ENSCPOG00000000429 4 retrocopies
Dasypus novemcinctus ENSDNOG0000000621431 retrocopies
Equus caballus ENSECAG000000015998 retrocopies
Echinops telfairi ENSETEG0000000685414 retrocopies
Felis catus ENSFCAG000000284027 retrocopies
Homo sapiens ENSG0000011230626 retrocopies
Gorilla gorilla ENSGGOG0000001223422 retrocopies
Gadus morhua ENSGMOG000000194551 retrocopy
Loxodonta africana ENSLAFG0000000793311 retrocopies
Macropus eugenii ENSMEUG000000042851 retrocopy
Microcebus murinus ENSMICG000000052525 retrocopies
Myotis lucifugus ENSMLUG000000011375 retrocopies
Macaca mulatta ENSMMUG000000132371 retrocopy
Monodelphis domestica ENSMODG000000175201 retrocopy
Mustela putorius furoENSMPUG000000147711 retrocopy
Mus musculus ENSMUSG000000619831 retrocopy
Nomascus leucogenys ENSNLEG000000146114 retrocopies
Oryctolagus cuniculus ENSOCUG0000000160614 retrocopies
Otolemur garnettii ENSOGAG0000000130920 retrocopies
Pongo abelii ENSPPYG0000001702026 retrocopies
Pelodiscus sinensis ENSPSIG000000034571 retrocopy
Pan troglodytes ENSPTRG0000001861825 retrocopies
Pteropus vampyrus ENSPVAG0000001720112 retrocopies
Rattus norvegicus ENSRNOG000000164115 retrocopies
Sorex araneus ENSSARG000000031702 retrocopies
Sarcophilus harrisii ENSSHAG000000089056 retrocopies
Sus scrofa ENSSSCG000000041778 retrocopies
Tarsius syrichta ENSTSYG0000001009724 retrocopies
Tursiops truncatus ENSTTRG0000000060911 retrocopies
Vicugna pacos ENSVPAG000000100824 retrocopies
Vicugna pacos ENSVPAG000000115043 retrocopies



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