RetrogeneDB ID:

retro_cpor_1528

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_93:5898794..5899184(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:AP3S1
Ensembl ID:ENSCPOG00000007192
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_1528
ATGATCAAAGCAATTCTCACCTTCAACAACCACAGGAAACCACAACTCTCAAATTCTACCAGCCCTAAGGTGAAGACAAA
CAAGAACTCATCAGGGAGACTTCCCACTTGGTATCTAAGAGAGATGAAAATGTTTGTAATTTACTACGAGGACTATTAAT
TGGAAGATCTGACAACAAAGTGATTTGCAGACATAACACAACACTATATTTTGTCTTCTGTGTGGTTTCTTCAGAAGGTG
AACTTGGCATTTAGGATATAATTCAAGTTTTGTGGAGACATTAGACAAATGTTTTGAAAATGTCTATGAACTGGATTTAA
TTTTCCATGTAAACAAAGTTTACAATATTCTTGTGGAAATGGTGATGGGGGAAGGGTATTGGAAACCAAC

ORF - retro_cpor_1528 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.94 %
Parental protein coverage: 68.91 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMIKAILIFNNHGKPRLS-KFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEGGLLIGGSDNKLIYRHYA
MIKAIL.FNNH.KP.LS.KFYQP..ED..Q..IRET.HLVSKRDENVCN.L.G.LLIG.SDNK.I.RH..
RetrocopyMIKAILTFNNHRKPQLS<KFYQP*GED-KQELIRETSHLVSKRDENVCNLLRG-LLIGRSDNKVICRHNT
ParentalTLYFVFCVDSSESELGILDLIQV-FVETLDKCFENVCELDLIFHVDKVHNILAEMVM-GGMVLETN
TLYFVFCV.SSE.ELGI.D.IQV.FVETLDKCFENV.ELDLIFHV.KV.NIL.EMVM.GG.VLETN
RetrocopyTLYFVFCVVSSEGELGI*DIIQV<FVETLDKCFENVYELDLIFHVNKVYNILVEMVM<GGRVLETN

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 18 .41 RPM
SRP017611_kidney 0 .00 RPM 7 .22 RPM
SRP017611_liver 0 .00 RPM 10 .66 RPM
SRP040447_lung 0 .08 RPM 9 .21 RPM
SRP040447_skeletal_muscle 0 .00 RPM 2 .91 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1528 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1528 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 24 parental genes, and 64 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000002031 retrocopy
Callithrix jacchus ENSCJAG000000167671 retrocopy
Cavia porcellus ENSCPOG00000007192 3 retrocopies
retro_cpor_1528 , retro_cpor_551, retro_cpor_779,
Felis catus ENSFCAG000000299203 retrocopies
Homo sapiens ENSG000001778793 retrocopies
Gorilla gorilla ENSGGOG000000168952 retrocopies
Loxodonta africana ENSLAFG000000153111 retrocopy
Macropus eugenii ENSMEUG000000106231 retrocopy
Microcebus murinus ENSMICG000000061574 retrocopies
Myotis lucifugus ENSMLUG000000027692 retrocopies
Macaca mulatta ENSMMUG000000152882 retrocopies
Mustela putorius furoENSMPUG000000007821 retrocopy
Mus musculus ENSMUSG000000244804 retrocopies
Otolemur garnettii ENSOGAG000000323761 retrocopy
Ochotona princeps ENSOPRG000000091762 retrocopies
Pongo abelii ENSPPYG000000157002 retrocopies
Pan troglodytes ENSPTRG000000171555 retrocopies
Pteropus vampyrus ENSPVAG000000065753 retrocopies
Rattus norvegicus ENSRNOG000000038291 retrocopy
Sarcophilus harrisii ENSSHAG000000011762 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000117591 retrocopy
Tupaia belangeri ENSTBEG000000047757 retrocopies
Tarsius syrichta ENSTSYG000000132319 retrocopies
Tursiops truncatus ENSTTRG000000008133 retrocopies



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