RetrogeneDB ID:

retro_cpor_837

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_3:67878063..67878306(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL22
Ensembl ID:ENSCPOG00000020139
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_837
AAGCACCTCTTTAAGTTCACCCCTGACTGTACACATCATGTGGAAGATGGAATCATGGATGCTGTCAATTTCAAACAATT
TTTCCAGGAGAGAATCAAGGTGAACTGCACAGTCAGGAATCTCAGCAGAAGTGTGGTCACCATTAAAAGGAGCAAGAGCA
AGATCAGTGTGTCTTCCAAGGTGTCTTTTTCCAAAAGGTATTTGAAATACCTCACCAAAAAGTATCTGAAGAACAATAAC
ATA

ORF - retro_cpor_837 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.84 %
Parental protein coverage: 63.28 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKQVLKFTLDCTHPVEDGIMDAANFEQFLQERIKVNGKAGNLGGGVVTIERSKSKITVTSEVPFSKRYLKY
K...KFT.DCTH.VEDGIMDA.NF.QF.QERIKVN....NL...VVTI.RSKSKI.V.S.V.FSKRYLKY
RetrocopyKHLFKFTPDCTHHVEDGIMDAVNFKQFFQERIKVNCTVRNLSRSVVTIKRSKSKISVSSKVSFSKRYLKY
ParentalLTKKYLKKNNL
LTKKYLK.NN.
RetrocopyLTKKYLKNNNI

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 34 .80 RPM
SRP017611_kidney 0 .00 RPM 57 .68 RPM
SRP017611_liver 0 .00 RPM 48 .31 RPM
SRP040447_lung 0 .00 RPM 65 .52 RPM
SRP040447_skeletal_muscle 0 .00 RPM 49 .24 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_837 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_837 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 11 parental genes, and 93 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000098647 retrocopies
Bos taurus ENSBTAG000000144234 retrocopies
Cavia porcellus ENSCPOG000000092151 retrocopy
Cavia porcellus ENSCPOG00000020139 2 retrocopies
retro_cpor_825, retro_cpor_837 ,
Gorilla gorilla ENSGGOG0000002773910 retrocopies
Macaca mulatta ENSMMUG0000001834712 retrocopies
Mustela putorius furoENSMPUG000000070876 retrocopies
Pongo abelii ENSPPYG0000000195111 retrocopies
Sus scrofa ENSSSCG000000033674 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000028324 retrocopies
Tarsius syrichta ENSTSYG0000000364932 retrocopies



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