RetrogeneDB ID:

retro_cpor_4

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_12:33437157..33437454(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000001357
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCPOG00000002336
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_4
ATGCCTAAGAGGGAGGTCAGCTTAGTCAAAGGGATGGCGAAGGAGGAGTCCAAGAGGAGATCTGCAAGGTTGTCCCCTAA
ACCTGCTCCTGAAAAAGTGGAAATGAAGCCAAGAAAGGCTGAAGGAAAGGATAAATCTTTGGACAAGAAAATGCAAGCAA
AAAGGAAAAGGGGAGAGGAGAAAAAACCATCTGAAGTGCCTAATCTAGAGACCAACCAAGGCTCACCTGCCAAAAATGGA
GAATCGAAAAACAAGGTGAGCTCAGCCTCTGACGAAGCAGAAGAGAAAGATGCCTAG

ORF - retro_cpor_4 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.18 %
Parental protein coverage: 97.03 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPKRKVSTAAARTAPAPKRRSARLSAKPAPAKVETKPKKAAGKDKSVDKKVQPKGKRGAKGKQAEAAHQE
MPKR.VS..........KRRSARLS.KPAP.KVE.KP.KA.GKDKS.DKK.Q.K.KRG...K..E....E
RetrocopyMPKREVSLVKGMAKEESKRRSARLSPKPAPEKVEMKPRKAEGKDKSLDKKMQAKRKRGEEKKPSEVPNLE
ParentalAKEDLPAENGEAKNAESAASDEAEEKEA
.....PA.NGE.KN..S.ASDEAEEK.A
RetrocopyTNQGSPAKNGESKNKVSSASDEAEEKDA

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 31 .40 RPM
SRP017611_kidney 0 .00 RPM 83 .33 RPM
SRP017611_liver 0 .00 RPM 23 .72 RPM
SRP040447_lung 0 .00 RPM 86 .23 RPM
SRP040447_skeletal_muscle 0 .00 RPM 18 .93 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_4 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_4 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 14 parental genes, and 170 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001410011 retrocopies
Bos taurus ENSBTAG0000001876812 retrocopies
Canis familiaris ENSCAFG0000001004512 retrocopies
Cavia porcellus ENSCPOG00000002336 7 retrocopies
Equus caballus ENSECAG000000190295 retrocopies
Homo sapiens ENSG000002055817 retrocopies
Monodelphis domestica ENSMODG000000209725 retrocopies
Mustela putorius furoENSMPUG000000085503 retrocopies
Mus musculus ENSMUSG0000004068113 retrocopies
Otolemur garnettii ENSOGAG0000001032935 retrocopies
Pongo abelii ENSPPYG0000001142625 retrocopies
Pan troglodytes ENSPTRG0000003142622 retrocopies
Rattus norvegicus ENSRNOG000000482268 retrocopies
Rattus norvegicus ENSRNOG000000509785 retrocopies



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