RetrogeneDB ID:

retro_ptro_2343

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:6:35464322..35464627(+)
Located in intron of:ENSPTRG00000018076
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPE1
Ensembl ID:ENSPTRG00000012774
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_2343
ATGGCGGGACCAGCATTTAGAAAGTTTCTTTCACTCTTTGACTGAATATTGGTTGAAAGGAGTGCAGCTGAAACTGTAAC
CAAAGGAGGCATTATGCCTCCAGGAAAATCTCAGGGAGAAGTATCACAAGCAGCAGTGGTAGCTGTTGCATCAGGCTCTA
AAGGAAAGGGTAGAGAGATTCGACCAATTAGCGTGGAAGTTGGAGACAAATTTCTTCTCCCAGAATATAGAGGCACCAAA
GTAGTTCTAGGTGACAGGATTATTTCTTATTTAGAGATGGTGACATTCTTGGAAAGAATGCAGAC

ORF - retro_ptro_2343 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.61 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAGQAFRKFLPLFDRVLVERSAAETVTKGGIMLPEKSQGKVLQATVVAVGSGSKGKGGEIQPVSVKVGDK
MAG.AFRKFL.LFD..LVERSAAETVTKGGIM.P.KSQG.V.QA.VVAV.SGSKGKG.EI.P.SV.VGDK
RetrocopyMAGPAFRKFLSLFD*ILVERSAAETVTKGGIMPPGKSQGEVSQAAVVAVASGSKGKGREIRPISVEVGDK
ParentalVLLPEYGGTKVVLDDK-DYFLFRDGDILGKYVD
.LLPEY.GTKVVL.D..DYFLFRDGDILGK..D
RetrocopyFLLPEYRGTKVVLGDR<DYFLFRDGDILGKNAD

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 .11 RPM 33 .00 RPM
SRP007412_cerebellum 0 .18 RPM 43 .05 RPM
SRP007412_heart 0 .15 RPM 125 .59 RPM
SRP007412_kidney 0 .10 RPM 129 .40 RPM
SRP007412_liver 0 .03 RPM 156 .86 RPM
SRP007412_testis 0 .21 RPM 45 .63 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2343 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2343 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2343 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3455
Gorilla gorilla retro_ggor_2331

Parental genes homology:
Parental genes homology involve 5 parental genes, and 53 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG0000001324627 retrocopies
Macaca mulatta ENSMMUG000000104911 retrocopy
Pongo abelii ENSPPYG000000258761 retrocopy
Pan troglodytes ENSPTRG00000012774 17 retrocopies
Sus scrofa ENSSSCG000000160787 retrocopies



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