RetrogeneDB ID:

retro_ptro_1220

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:17:27080064..27080504(-)
Located in intron of:ENSPTRG00000008956
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NME4
Ensembl ID:ENSPTRG00000007541
Aliases:None
Description:NME/NM23 nucleoside diphosphate kinase 4 [Source:HGNC Symbol;Acc:7852]


Retrocopy-Parental alignment summary:






>retro_ptro_1220
GGCTCAGGAGGACCCTTCTTGATCCAGGAGTGGACCCTGGTCTCATTGAAGCCAGTTGGGGTCTTGTGGCGGCCTGTTAG
GGATGTGATCCAGCGCTTTGGAGGCAGGGCTTCAAGCTGGTAGGGATGAAGATTCTGTGGCCGGCCAGAAAGCGTCCTTG
CTGAACACTACCAGGACCTGCGAAGGAAGCCCCTCTACCCAGCCCTCCTTAGCTATGTGAGCTCCAGGCCTGTTGATGGC
CGTGGTCTGGGAAGGGTACAAGGTGATCCATGCCTCGAGGGCCATGATAGATACACTGACAGGGTTGAGGCTGACTCTGT
GACCATATGGGGAGACTTCAGCGACGTCCACATCAGCAGGAACATCATTCACACCAGCTATTCAGGGTAGGGGGTCAGAA
AGAGATCCAGCTGTGGTTTGAAAGCAGTAAGCTGGTGAAC

ORF - retro_ptro_1220 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.13 %
Parental protein coverage: 88.48 %
Number of stop codons detected: 0
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalGGGGPSWTRERTLVAVKPDGVQRRLVGDVIQRFE-RRGFTLVGMKMLQA-PESVLAEHYQDLRRKPFYPA
G.GGP....E.TLV..KP.GV..R.V.DVIQRF..R.GF.LVGMK.L...PESVLAEHYQDLRRKP.YPA
RetrocopyGSGGPFLIQEWTLVSLKPVGVLWRPVRDVIQRFG<RQGFKLVGMKILWP>PESVLAEHYQDLRRKPLYPA
ParentalLIRYMSSGPV-VAMVWEGYNVVRASRAMIG-HTDSAEAAPGTIRGDFS-VHISRNVIHASDS-VEGAQRE
L..Y.SS.PV..A.VWEGY.V..ASRAMI...TD..EA...TI.GDFS.VHISRN.IH.S.S...G.Q.E
RetrocopyLLSYVSSRPV>MAVVWEGYKVIHASRAMID<YTDRVEADSVTIWGDFSDVHISRNIIHTSYS<RVGGQKE
ParentalIQLWFQSSELVS
IQLWF.SS.LV.
RetrocopyIQLWFESSKLVN

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 .00 RPM 44 .70 RPM
SRP007412_cerebellum 0 .00 RPM 28 .93 RPM
SRP007412_heart 0 .00 RPM 46 .93 RPM
SRP007412_kidney 0 .00 RPM 63 .68 RPM
SRP007412_liver 0 .00 RPM 62 .00 RPM
SRP007412_testis 0 .11 RPM 18 .97 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1220 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1220 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1220 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 22 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000070773 retrocopies
Canis familiaris ENSCAFG000000196774 retrocopies
Cavia porcellus ENSCPOG000000064961 retrocopy
Echinops telfairi ENSETEG000000148751 retrocopy
Felis catus ENSFCAG000000083003 retrocopies
Homo sapiens ENSG000001032021 retrocopy
Gorilla gorilla ENSGGOG000000045121 retrocopy
Macropus eugenii ENSMEUG000000054555 retrocopies
Myotis lucifugus ENSMLUG000000100611 retrocopy
Macaca mulatta ENSMMUG000000006121 retrocopy
Mustela putorius furoENSMPUG000000160173 retrocopies
Mus musculus ENSMUSG000000241771 retrocopy
Nomascus leucogenys ENSNLEG000000080681 retrocopy
Otolemur garnettii ENSOGAG000000258081 retrocopy
Pongo abelii ENSPPYG000000069081 retrocopy
Pan troglodytes ENSPTRG00000007541 1 retrocopy
retro_ptro_1220 ,
Pan troglodytes ENSPTRG000000094151 retrocopy
Rattus norvegicus ENSRNOG000000491521 retrocopy
Sus scrofa ENSSSCG000000079862 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000047981 retrocopy
Tursiops truncatus ENSTTRG000000091572 retrocopies
Vicugna pacos ENSVPAG000000103161 retrocopy



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