RetrogeneDB ID:

retro_cpor_90

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_181:667515..667842(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000012061
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS15A
Ensembl ID:ENSCPOG00000021695
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_90
GCTGATGCTCTCAAGAGCATCAACAATGCTGAAAAGAGAGGCAAATGCCAGGTCCTTATTAGACCATGCTCCAAAGTCAT
CGTCCGGTTTCTAACTGTGACGATGAAGCATAGTTACATTGGCGAATTTGAAATCATTGATGATCACAGGGCTGGAAAAA
TTGTTGTGAACCTCACAGGCAGGTTAAATAAGTGTGGTGTGATCAGCCCCAGGTTTGATGTGCAACTGAAAGACCTGGAA
AAATGGCAGAATAATCTGCTCCCATCCTGTCAGTTTGGTTTCATTGTATTGACCACCTCAGCTGGCATCATGGACCATGA
AGAAGCA

ORF - retro_cpor_90 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.33 %
Parental protein coverage: 83.85 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalADALKSINNAEKRGKRQVLIRPCSKVIVRFLTVMMKHGYIGEFEIIDDHRAGKIVVNLTGRLNKCGVISP
ADALKSINNAEKRGK.QVLIRPCSKVIVRFLTV.MKH.YIGEFEIIDDHRAGKIVVNLTGRLNKCGVISP
RetrocopyADALKSINNAEKRGKCQVLIRPCSKVIVRFLTVTMKHSYIGEFEIIDDHRAGKIVVNLTGRLNKCGVISP
ParentalRFDVQLKDLEKWQNNLLPSRQFGFIVLTTSAGIMDHEEA
RFDVQLKDLEKWQNNLLPS.QFGFIVLTTSAGIMDHEEA
RetrocopyRFDVQLKDLEKWQNNLLPSCQFGFIVLTTSAGIMDHEEA

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 .06 RPM 59 .47 RPM
SRP017611_kidney 0 .42 RPM 116 .52 RPM
SRP017611_liver 0 .00 RPM 81 .96 RPM
SRP040447_lung 0 .28 RPM 209 .71 RPM
SRP040447_skeletal_muscle 0 .35 RPM 193 .63 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_90 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_90 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 21 parental genes, and 288 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001108318 retrocopies
Bos taurus ENSBTAG000000207335 retrocopies
Callithrix jacchus ENSCJAG000000200716 retrocopies
Cavia porcellus ENSCPOG00000021695 12 retrocopies
Dasypus novemcinctus ENSDNOG0000000834145 retrocopies
Dipodomys ordii ENSDORG000000015575 retrocopies
Equus caballus ENSECAG000000192932 retrocopies
Homo sapiens ENSG0000013441937 retrocopies
Gorilla gorilla ENSGGOG0000002629932 retrocopies
Gadus morhua ENSGMOG000000058621 retrocopy
Latimeria chalumnae ENSLACG000000114761 retrocopy
Loxodonta africana ENSLAFG0000002699613 retrocopies
Microcebus murinus ENSMICG0000001224120 retrocopies
Macaca mulatta ENSMMUG000000055933 retrocopies
Oryctolagus cuniculus ENSOCUG0000000017925 retrocopies
Otolemur garnettii ENSOGAG0000001319914 retrocopies
Pongo abelii ENSPPYG000000071392 retrocopies
Pan troglodytes ENSPTRG000000078232 retrocopies
Pteropus vampyrus ENSPVAG0000000290114 retrocopies
Rattus norvegicus ENSRNOG000000183205 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000002522226 retrocopies



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