RetrogeneDB ID:

retro_cpor_321

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_123:3512864..3513367(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCPOG00000019917
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_321
ATGAACCCTTGGTCTCTTTATTTAAATATGGATCCACGATATCTTGTGCAGGATACTGATGCATTTATTTTACTGACTGG
AGCTAATAAAACCCAAGGCAGGTTTGAAATGGCCTTCTCTGCCACTGGGGGATGTTGCATGACGGGCACTGCATTTGTAG
CAGTGAACCGTCTTCAGCTAGGATTGAAGGAAACCCAGAATATGGCCTGGTCCAAACCAAGAAATGGACAGGTTTTGAAT
ATGGTGACTAGGCAAGGGGCACTGTGGGCCAGTGTTTTTGGTCCGTTGGCTTTGCTCGACAGTGCATTTGGTGTTATCAT
TGAGAAAACACAAGGAGCAGAAGATAATCTGAACACTGGCAGCCAGAACCATGGCAGGCATCAGCGCACAGGTGGGCTTC
CAGGGGTTGCATGAGGGAGTCTGGCAGGCATAACACTACCAGTCTGCGTGCACTCTGTGACAACTGGGAGCACAGGAAAG
GCTCCTTGCTCCCCCAGCCACTC

ORF - retro_cpor_321 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.67 %
Parental protein coverage: 81.82 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMNPLSPYLNVDPRYLVQDTDEFILPTGANKTRGRFELAFFTIGGCCMTGAAFGAVNGLRLGLKETQNMAW
MNP.S.YLN.DPRYLVQDTD.FIL.TGANKT.GRFE.AF...GGCCMTG.AF.AVN.L.LGLKETQNMAW
RetrocopyMNPWSLYLNMDPRYLVQDTDAFILLTGANKTQGRFEMAFSATGGCCMTGTAFVAVNRLQLGLKETQNMAW
ParentalSKPRNVQILNMVTRQGALWANTLGSLALLYSAFGVIIEKTRGAEDDLNTVAAGTMTGMLYKCTGGLRGVA
SKPRN.Q.LNMVTRQGALWA...G.LALL.SAFGVIIEKT.GAED.LNT...G.........TGGL.GVA
RetrocopySKPRNGQVLNMVTRQGALWASVFGPLALLDSAFGVIIEKTQGAEDNLNT---GSQNHGRHQRTGGLPGVA
ParentalRGGLAGLTL-TGLYALYNNWEHMKGSLLHQSL
.G.LAG.TL.T.L.AL..NWEH.KGSLL.Q.L
Retrocopy*GSLAGITL<TSLRALCDNWEHRKGSLLPQPL

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 .25 RPM
SRP017611_kidney 0 .00 RPM 32 .66 RPM
SRP017611_liver 0 .00 RPM 17 .67 RPM
SRP040447_lung 0 .00 RPM 14 .63 RPM
SRP040447_skeletal_muscle 0 .00 RPM 40 .36 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_321 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_321 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 15 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000075011 retrocopy
Canis familiaris ENSCAFG000000294771 retrocopy
Choloepus hoffmanni ENSCHOG000000070731 retrocopy
Callithrix jacchus ENSCJAG000000133361 retrocopy
Cavia porcellus ENSCPOG00000019917 2 retrocopies
retro_cpor_1013, retro_cpor_321 ,
Monodelphis domestica ENSMODG000000026612 retrocopies
Mus musculus ENSMUSG000000137011 retrocopy
Oryctolagus cuniculus ENSOCUG000000005251 retrocopy
Otolemur garnettii ENSOGAG000000153931 retrocopy
Ochotona princeps ENSOPRG000000052552 retrocopies
Procavia capensis ENSPCAG000000159141 retrocopy
Rattus norvegicus ENSRNOG000000198113 retrocopies
Sorex araneus ENSSARG000000103351 retrocopy
Sus scrofa ENSSSCG000000252761 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000070411 retrocopy



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