RetrogeneDB ID:

retro_cpor_972

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_37:22630182..22630538(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP5H
Ensembl ID:ENSCPOG00000004022
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_972
AGGTTGGCTGCTCTGGCTGAGAATCCACCAGTGACCAACTGGGCTTACTCTAAGGTCAGTGTGGCCAAGGCAGGCTTGGT
GGATGACTTGGAAGCAAAGTTTAATGCCCTGAACGTCCCTGTGCCAGTGGATAAATGCTGATGGATGGATGCTGATGGAA
AGGAAGATGTGGAAGGTTGCTCTGAGTTTGTCTCTCTCTCAAAGGCCGGGTTGTACAATATGAGAAACAGCTGGAGAAAA
TGAGCAGCATAGTTCCATTTGATCAGGTGACCACTGAGGATTTGAATGAAGTCTTCCTAGAAACCAAAATAGTTAAGAAG
TATCACTATTGGCCTCACCAGCCAATTGAGAATTTA

ORF - retro_cpor_972 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.49 %
Parental protein coverage: 77.56 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalRLAALSEKPPAIDWAYYKANVAKAGLVDEFEKKFNALKVPVPEDKYTALVDAEEKEDVKSCAEFVSLSKA
RLAAL.E.PP...WAY.K..VAKAGLVD..E.KFNAL.VPVP.DK.....DA..KEDV..C.EFVSLSKA
RetrocopyRLAALAENPPVTNWAYSKVSVAKAGLVDDLEAKFNALNVPVPVDK-C*WMDADGKEDVEGCSEFVSLSKA
Parental-RIVEYEKQLEKMNNIIPFDQMTIEDLNEVFPETKLDKKKYPYWPHQPIENL
.R.V.YEKQLEKM..I.PFDQ.T.EDLNEVF.ETK...KKY.YWPHQPIENL
Retrocopy<RVVQYEKQLEKMSSIVPFDQVTTEDLNEVFLETKI-VKKYHYWPHQPIENL

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 55 .27 RPM
SRP017611_kidney 0 .00 RPM 149 .91 RPM
SRP017611_liver 0 .00 RPM 93 .28 RPM
SRP040447_lung 0 .00 RPM 37 .83 RPM
SRP040447_skeletal_muscle 0 .00 RPM 158 .04 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_972 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_972 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 29 parental genes, and 113 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000091156 retrocopies
Bos taurus ENSBTAG000000212275 retrocopies
Canis familiaris ENSCAFG000000047031 retrocopy
Callithrix jacchus ENSCJAG0000001462215 retrocopies
Cavia porcellus ENSCPOG00000004022 3 retrocopies
retro_cpor_1429, retro_cpor_547, retro_cpor_972 ,
Dasypus novemcinctus ENSDNOG000000069132 retrocopies
Equus caballus ENSECAG000000094872 retrocopies
Echinops telfairi ENSETEG000000032178 retrocopies
Felis catus ENSFCAG000000228882 retrocopies
Homo sapiens ENSG000001678634 retrocopies
Gorilla gorilla ENSGGOG000000137164 retrocopies
Macropus eugenii ENSMEUG000000093461 retrocopy
Microcebus murinus ENSMICG000000174844 retrocopies
Myotis lucifugus ENSMLUG000000106207 retrocopies
Macaca mulatta ENSMMUG000000116471 retrocopy
Mustela putorius furoENSMPUG000000140489 retrocopies
Mus musculus ENSMUSG000000345666 retrocopies
Nomascus leucogenys ENSNLEG000000005614 retrocopies
Oryctolagus cuniculus ENSOCUG000000155372 retrocopies
Otolemur garnettii ENSOGAG000000019904 retrocopies
Procavia capensis ENSPCAG000000153302 retrocopies
Pongo abelii ENSPPYG000000086154 retrocopies
Pan troglodytes ENSPTRG000000096284 retrocopies
Rattus norvegicus ENSRNOG000000036261 retrocopy
Sorex araneus ENSSARG000000133703 retrocopies
Sarcophilus harrisii ENSSHAG000000187082 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000151542 retrocopies
Tupaia belangeri ENSTBEG000000125453 retrocopies
Tursiops truncatus ENSTTRG000000026182 retrocopies



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