RetrogeneDB ID:

retro_cpor_259

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_11:23816359..23816913(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DNAJB6
Ensembl ID:ENSCPOG00000013953
Aliases:None
Description:DnaJ (Hsp40) homolog, subfamily B, member 6 [Source:HGNC Symbol;Acc:14888]


Retrocopy-Parental alignment summary:






>retro_cpor_259
GAGAAACAGCAGAAATTCAGACAAGTTGCTAAGGCATATATGGTGTTATCAGATGTTAAAAAAAGGAACATCTGTGACAA
ATATGGCCAAGAAAGATTAAATGGTGGAGGAGGAAGTGAAAGTCACTTTGACAGTTCATTTGAGCCAGGTTTCCATTGGA
TATCCCAGATAATTCCTTCAGGGAATGTTCTGGTAAAAAAGGACCTTTTCTCATTCAGCTTCAAAGCCCTATTTGAAGAT
TTCTTTGGGAATAAAAGGAGTTCCCAAGGAAGTAGAGGCCACATTGTGACCTTTTTCTCTGCTTTCCGTGAATTTTTATC
ATTTCGAGTTGGATTTTCTTGACTTGATACAGGATTTACTTCATTTGGATCCATATATTACGGGGTTTCATTTCATTCTC
TTCCACCTCATTTAGCAGCAGTGAGATGGGCAACTTCCAATCTATATCAGCTTCTACTAAAATAGGGGAAGCAAAATTAC
CACAAAGAGAATTGTCAAGAATGGTCCAGAAAGAAGTTGAAGATGTACAGTTAAAATCCTTAACCATAAATGGT

ORF - retro_cpor_259 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.73 %
Parental protein coverage: 82.68 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalEAERKFKQVAEAYEVLSDAKKRDIYDKYGKEGLNGGGGGGSHFDSPFEFGFTFRN-PDDVFREFFGGRDP
E...KF.QVA.AY.VLSD.KKR.I.DKYG.E.LNGGGG..SHFDS.FE.GF.....PD..FRE..G...P
RetrocopyEKQQKFRQVAKAYMVLSDVKKRNICDKYGQERLNGGGGSESHFDSSFEPGFHWIS<PDNSFRECSGKKGP
Parental-FSFDFFEDPFEDLFGNRRGPRGSRNRGTGSFFSAFSGFPSFGGGFSAFDTGFTSFGSLGHG-GLTSFSS
.FSF..F...FED.FGN.R...GSR......FFSAF..F.SF..GFS..DTGFTSFGS...G.G..SFSS
Retrocopy>FSFS-FKALFEDFFGNKRSSQGSRGH-IVTFFSAFREFLSFRVGFS*LDTGFTSFGSIYYG<GFISFSS
ParentalTSFGGSGMGNFKSISTSTKIVNGRKITTKRIVENGQERVEVEEDGQLKSLTING
TSF..S.MGNF.SIS.STKI....K..........Q..VE...D.QLKSLTING
RetrocopyTSFSSSEMGNFQSISASTKI-GEAKLPQRELSRMVQKEVE---DVQLKSLTING

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 .40 RPM 60 .05 RPM
SRP017611_kidney 0 .21 RPM 46 .80 RPM
SRP017611_liver 0 .09 RPM 32 .38 RPM
SRP040447_lung 0 .08 RPM 52 .84 RPM
SRP040447_skeletal_muscle 0 .07 RPM 39 .10 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_259 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_259 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 26 parental genes, and 121 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000013323 retrocopies
Bos taurus ENSBTAG000000007713 retrocopies
Canis familiaris ENSCAFG000000051746 retrocopies
Callithrix jacchus ENSCJAG000000052887 retrocopies
Cavia porcellus ENSCPOG00000013953 17 retrocopies
Equus caballus ENSECAG000000090052 retrocopies
Felis catus ENSFCAG000000156542 retrocopies
Homo sapiens ENSG000001059939 retrocopies
Gorilla gorilla ENSGGOG000000047036 retrocopies
Loxodonta africana ENSLAFG000000133844 retrocopies
Microcebus murinus ENSMICG000000097601 retrocopy
Myotis lucifugus ENSMLUG000000091234 retrocopies
Macaca mulatta ENSMMUG000000031766 retrocopies
Mustela putorius furoENSMPUG000000097974 retrocopies
Mus musculus ENSMUSG000000291316 retrocopies
Nomascus leucogenys ENSNLEG000000013805 retrocopies
Oryctolagus cuniculus ENSOCUG000000000642 retrocopies
Otolemur garnettii ENSOGAG000000106402 retrocopies
Pongo abelii ENSPPYG000000182284 retrocopies
Pelodiscus sinensis ENSPSIG000000181021 retrocopy
Pteropus vampyrus ENSPVAG000000001551 retrocopy
Rattus norvegicus ENSRNOG000000103536 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000029647 retrocopies
Tupaia belangeri ENSTBEG000000095867 retrocopies
Tarsius syrichta ENSTSYG000000054484 retrocopies
Tursiops truncatus ENSTTRG000000139292 retrocopies



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