RetrogeneDB ID:

retro_cpor_798

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_28:25863092..25863509(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PPIH
Ensembl ID:ENSCPOG00000008214
Aliases:None
Description:Peptidyl-prolyl cis-trans isomerase [Source:UniProtKB/TrEMBL;Acc:H0VBU7]


Retrocopy-Parental alignment summary:






>retro_cpor_798
ATGGCAATGGCTAATATAATCCCCATAAACCCTGTGTTGTTTTCATGTCAGTGTTGGTGGCTAGAAAGTTGGCTGCATAA
AGATAGAAATGTTTGAAGGTGTCATGCTGAAAACAGCCAAGTATTTCAGGCAATTTTGCACTGGAGAATTCCCAAAAGAT
GGAGCTCCAATAGGGTATAAGGAAAGTACCTTCCACAGGGGCATAAAGGATTTCATGATTCAGGGTTAAGATTTTGTTAA
TGGAGATGGTACTGGAGTTGCCAGTATTTACAAGAGCCCATTTGCACGCAAAAATCTGAGACTCAGATCCTCAGCTCCTG
GGCTACTTTCCATGGCAAACAGTGGTCCCAGTACAAATGGCTGTCAGCTCTTTATCACCTGCTCCAAGTGGCACTGTTGG
ATGGGAAGCATGGAGTG

ORF - retro_cpor_798 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.03 %
Parental protein coverage: 79.1 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMAVANS-SPVNPVVFF-DVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRV
MA.AN...P..P.V.F..VS.GG..VG..KIE.F..V..KTA..FRQFCTGEF.KDG.PIGYK.STFHR.
RetrocopyMAMANI<NPHKPCVVF<HVSVGG*KVGCIKIEMFEGVMLKTAKYFRQFCTGEFPKDGAPIGYKESTFHRG
ParentalIKDFMIQGGDFVNGDGTGVASIYRGPFADENFKLRHSAPGLLSMANSGPSTNGCQFFITCSK-CDWLDGK
IKDFMIQG.DFVNGDGTGVASIY..PFA..N..LR.SAPGLLSMANSGPSTNGCQ.FITCSK....LDGK
RetrocopyIKDFMIQG*DFVNGDGTGVASIYKSPFARKNLRLRSSAPGLLSMANSGPSTNGCQLFITCSK<VALLDGK
ParentalHVV
H.V
RetrocopyHGV

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 9 .38 RPM
SRP017611_kidney 0 .00 RPM 11 .83 RPM
SRP017611_liver 0 .00 RPM 9 .66 RPM
SRP040447_lung 0 .00 RPM 11 .80 RPM
SRP040447_skeletal_muscle 0 .00 RPM 5 .51 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_798 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_798 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 19 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000005261 retrocopy
Bos taurus ENSBTAG000000045901 retrocopy
Callithrix jacchus ENSCJAG000000031455 retrocopies
Cavia porcellus ENSCPOG00000008214 8 retrocopies
Dipodomys ordii ENSDORG000000161523 retrocopies
Homo sapiens ENSG000001719602 retrocopies
Gorilla gorilla ENSGGOG000000225072 retrocopies
Macropus eugenii ENSMEUG000000016911 retrocopy
Myotis lucifugus ENSMLUG000000254002 retrocopies
Macaca mulatta ENSMMUG000000131291 retrocopy
Mustela putorius furoENSMPUG000000139662 retrocopies
Nomascus leucogenys ENSNLEG000000123132 retrocopies
Oryctolagus cuniculus ENSOCUG000000114531 retrocopy
Procavia capensis ENSPCAG000000111391 retrocopy
Pongo abelii ENSPPYG000000014672 retrocopies
Pan troglodytes ENSPTRG000000006142 retrocopies
Pteropus vampyrus ENSPVAG000000055001 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000001152 retrocopies
Tarsius syrichta ENSTSYG000000031822 retrocopies



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