RetrogeneDB ID:

retro_cpor_167

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_1:3520671..3521062(+)
Located in intron of:ENSCPOG00000014446
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL26
Ensembl ID:ENSCPOG00000001315
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_167
AAGGCAAGGCATTTCAATGCACCTTCACACATTCGCAGGAAGATTATGTCTTCCCCTCTTTCCAAAGAGCTGAGACAGAA
ATACAATATTCAATCTATGCCCATCCAAAAGGATGATGAGGTTCAGGTTGTGCGAGGACACTATAAAGGTCAGCAGATTG
GGAAAGTAGTCCAAGTTTACAGGGAAGTAAGTCATCTACATTGAACGGGTGCAGCAGGAAAAAGCAAATGTTACCACTGT
CCATGTGGGCATTCACCCCAGCAAGGTGGTTATCACCAGGCTAAAACTGGACAAAGACCGCAAAAAGATCCTGGAACAGA
AAGCCAAGTCTCGCCAAGTAGGAAAGGAAAAGGGCAAATACAAGGAAGAGACAATTGAGAAGATGGAGGAG

ORF - retro_cpor_167 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.61 %
Parental protein coverage: 90.34 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQ-IGKVVQVYRKKYVIYIE
..RHFNAPSHIRRKIMSSPLSKELRQKYN..SMPI.KDDEVQVVRGHYKGQQ..GK.......K.VIYIE
RetrocopyKARHFNAPSHIRRKIMSSPLSKELRQKYNIQSMPIQKDDEVQVVRGHYKGQQ>LGK*SK-FTGK*VIYIE
ParentalRVQREKANGTTVHVGIHPSKVVITRLKLDKDRKKILERKAKSRQVGKEKGKYKEETIEKMQE
RVQ.EKAN.TTVHVGIHPSKVVITRLKLDKDRKKILE.KAKSRQVGKEKGKYKEETIEKM.E
RetrocopyRVQQEKANVTTVHVGIHPSKVVITRLKLDKDRKKILEQKAKSRQVGKEKGKYKEETIEKMEE

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 192 .45 RPM
SRP017611_kidney 0 .00 RPM 220 .68 RPM
SRP017611_liver 0 .04 RPM 156 .48 RPM
SRP040447_lung 0 .00 RPM 355 .56 RPM
SRP040447_skeletal_muscle 0 .08 RPM 353 .86 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_167 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_167 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 17 parental genes, and 116 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000024537 retrocopies
Bos taurus ENSBTAG000000123442 retrocopies
Callithrix jacchus ENSCJAG000000143728 retrocopies
Cavia porcellus ENSCPOG00000001315 10 retrocopies
Homo sapiens ENSG0000016197027 retrocopies
Gorilla gorilla ENSGGOG000000239444 retrocopies
Macropus eugenii ENSMEUG000000098917 retrocopies
Myotis lucifugus ENSMLUG000000021761 retrocopy
Macaca mulatta ENSMMUG0000000344822 retrocopies
Monodelphis domestica ENSMODG000000062012 retrocopies
Nomascus leucogenys ENSNLEG000000099811 retrocopy
Otolemur garnettii ENSOGAG000000170703 retrocopies
Pan troglodytes ENSPTRG000000087423 retrocopies
Rattus norvegicus ENSRNOG000000042143 retrocopies
Sarcophilus harrisii ENSSHAG000000068901 retrocopy
Sus scrofa ENSSSCG000000288509 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000219236 retrocopies



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