RetrogeneDB ID:

retro_cpor_217

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_10:19182195..19182611(-)
Located in intron of:ENSCPOG00000003146
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NAA50
Ensembl ID:ENSCPOG00000014169
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_217
GGACATGTAACAACACACAGTATCAAACAGCTGCAGGGGTAAGCCAGGGCATCTTTCCAGTAAGCTATAATGACAAGTTT
TACAAGGATGTGCTGAAGGTTGGCGAGCTAGCAAAACTTGCCTATTTCAATGACATTATTAGAGGTGCAGTATGCTGCAG
GATAGATCATCCACAGAATCAGAAAAGCCTGTACATCAAGACACTAGGATGTGTTATACCTTACTGAAGGCTAAGAATTG
GAACTAAAATGTCAAATCACATCTTAAACATATGTGAAAAAGATGGTACTTTTGAACACTATCTGATTGTCCAGATCAAC
AAGGAGCCAGCAATTAACTTCTGCAGGAAATTTGACTTTGAGATTACTGAGACAAAGAACTACTACATGGGAGTAGAGCC
TGCCGGTGCTCATGTG

ORF - retro_cpor_217 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.24 %
Parental protein coverage: 83.43 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGDVTPHNIKQLKR-LNQVIFPVSYNDKFYKDVLEVGELAKLAYFNDIAVGAVCCRVDHSQNQKRLYIMTL
G.VT.H.IKQL.....Q.IFPVSYNDKFYKDVL.VGELAKLAYFNDI..GAVCCR.DH.QNQK.LYI.TL
RetrocopyGHVTTHSIKQLQG<VSQGIFPVSYNDKFYKDVLKVGELAKLAYFNDIIRGAVCCRIDHPQNQKSLYIKTL
ParentalGCLAPYRRLGIGTKMLNHVLNICEKDGTFDNIYLHVQISNESAIDFYRKFGFEIIETKKNYYKRIEPADA
GC..PY.RL.IGTKM.NH.LNICEKDGTF...YL.VQI..E.AI.F.RKF.FEI.ET.KNYY...EPA.A
RetrocopyGCVIPY*RLRIGTKMSNHILNICEKDGTFEH-YLIVQINKEPAINFCRKFDFEITET-KNYYMGVEPAGA
ParentalHV
HV
RetrocopyHV

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 17 .02 RPM
SRP017611_kidney 0 .00 RPM 23 .87 RPM
SRP017611_liver 0 .00 RPM 29 .73 RPM
SRP040447_lung 0 .00 RPM 26 .71 RPM
SRP040447_skeletal_muscle 0 .00 RPM 82 .56 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_217 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_217 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 7 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG00000014169 6 retrocopies
Gorilla gorilla ENSGGOG000000065892 retrocopies
Loxodonta africana ENSLAFG000000040231 retrocopy
Oryctolagus cuniculus ENSOCUG000000064672 retrocopies
Otolemur garnettii ENSOGAG000000111971 retrocopy
Procavia capensis ENSPCAG000000097802 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000094381 retrocopy



Copyright © RetrogeneDB 2014-2017