RetrogeneDB ID:

retro_ptro_378

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:1:191979716..191979906(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS28
Ensembl ID:ENSPTRG00000040141
Aliases:None
Description:ribosomal protein S28 [Source:HGNC Symbol;Acc:10418]


Retrocopy-Parental alignment summary:






>retro_ptro_378
GACACCAGCCATGTGCAGCCTATCTAGCTAGCCAGGGTCACCAAGGTCCTGGGCAGAACCAGCTCTCAGGGACAGTGCAT
GCGGGAATTTATAGACACAAGCCACTCCATCATCCACAGTGTGAAAGGCCCCATGCGCAAGGGCTATGTGCTCACCCTGT
TTGGAGTCAGAGCGAGAGGCCTGGAGGTTG

ORF - retro_ptro_378 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.53 %
Parental protein coverage: 97.1 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTL-LESEREARRL
DTS.VQPI.LARVTKVLGRT.SQGQC.....EF..DTS.SII..VKGP.R.G.VLTL.LESEREA.RL
RetrocopyDTSHVQPI*LARVTKVLGRTSSQGQCMR---EFI-DTSHSIIHSVKGPMRKGYVLTL>LESEREAWRL

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
SRP007412_brain_prefrontal_cortex 0 .02 RPM 177 .49 RPM
SRP007412_cerebellum 0 .00 RPM 71 .02 RPM
SRP007412_heart 0 .00 RPM 67 .79 RPM
SRP007412_kidney 0 .00 RPM 248 .76 RPM
SRP007412_liver 0 .00 RPM 135 .03 RPM
SRP007412_testis 0 .00 RPM 11 .07 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_378 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_378 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_378 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_505

Parental genes homology:
Parental genes homology involve 7 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000002339279 retrocopies
Loxodonta africana ENSLAFG000000299232 retrocopies
Macaca mulatta ENSMMUG000000288953 retrocopies
Monodelphis domestica ENSMODG000000038901 retrocopy
Mus musculus ENSMUSG000000672883 retrocopies
Pan troglodytes ENSPTRG00000040141 6 retrocopies
Rattus norvegicus ENSRNOG000000428862 retrocopies



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